MultiBlast Query Service v2.0.0

Resources

Lists the current user's collected blast query jobs.

Parameters

Parameter	Type	Description
Query
site Target Site	string	Optionally filters the results of the job list endpoint down to only records relevant to the specified `TargetSite`.

curl -X GET \
  undefined/jobs?site=<value>

Parameter	Type	Description
[]	object	Inherits: object
[].queryJobID* Query Job ID	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
[].status* Job Status	string	Enum: queued in-progress complete failed expired Inherits: lib.JobStatus
[].site* Target Site	string	Enum: AmoebaDB CryptoDB FungiDB GiardiaDB HostDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.TargetSite
[].createdOn* Created On	datetime	Job creation timestamp.
[].userMeta User Metadata	object	Inherits: object
[].userMeta.summary Brief Summary	string	Brief, user defined summary or tagline for the job. Max. length: 512
[].userMeta.description Long Description	string	Longform, user provided description of the job.

Response Body

[
  {
    "queryJobID": "9f444b23ceec3ee5588cc4c784c16696",
    "site": "PlasmoDB",
    "status": "expired",
    "createdOn": "2020-10-31T23:00:00Z"
  },
  {
    "queryJobID": "bc49f1a3bc36cd15b84890439d19d395",
    "site": "TriTrypDB",
    "status": "complete",
    "createdOn": "2020-10-31T23:00:00Z",
    "userMeta": {
      "summary": "A blast job"
    }
  },
  {
    "queryJobID": "297a61dda47317f11d8e50e6ab8508c9",
    "site": "VectorBase",
    "status": "failed",
    "createdOn": "2020-10-31T23:00:00Z",
    "userMeta": {
      "summary": "Another blast job.",
      "description": "This job will fail."
    }
  }
]

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Creates a new blast query job.

curl -X POST \
  -H "Content-type: multipart/form-data"
  -d @file \
  undefined/jobs

Parameter	Type	Description
config* Query Job Request	object	Inherits: object
config.jobConfig* Job Config	object	Job Configuration. Inherits: lib.QueryJobConfig
config.jobConfig.site* Target Site	string	Enum: AmoebaDB CryptoDB FungiDB GiardiaDB HostDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.TargetSite
config.jobConfig.targets* Query Targets	array
config.jobConfig.targets[]	object	Inherits: lib.QueryJobTarget
config.jobConfig.targets[].targetDisplayName*	string	Blast target display name, e.g. organism name.
config.jobConfig.targets[].targetFile*	string	Target blast database file.
config.jobConfig.query Blast Query	string	For Requests Inline query definition. This field is to be used for non-file-upload blast queries. If this field is not set, a query file must be uploaded for the request to be valid. For Responses This field will be omitted.
config.jobConfig.addToUserCollection Add to Collection	boolean	Adds this job to the users collection of jobs. The user's collection of jobs is what is returned by the `/jobs` endpoint.
config.blastConfig* Blast Tool Config	object	Blast Tool Configuration. Implemented by one of: BlastNConfig BlastPConfig BlastXConfig DeltaBlastConfig PSIBlastConfig RPSBlastConfig RPSTBlastNConfig TBlastNConfig TBlastXConfig Discriminator: tool Inherits: lib.BlastQueryConfig
config.blastConfig.tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
config.blastConfig.queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
config.blastConfig.queryLocation.start*	integer	Format: long
config.blastConfig.queryLocation.stop*	integer	Format: long
config.blastConfig.eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
config.blastConfig.softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
config.blastConfig.lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
config.blastConfig.queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
config.userMeta User Metadata	object	Inherits: lib.QueryJobUserMeta
config.userMeta.summary Brief Summary	string	Brief, user defined summary or tagline for the job. Max. length: 512
config.userMeta.description Long Description	string	Longform, user provided description of the job.
query Query File	file	Optional file upload parameter for uploading multi-blast queries. IMPORTANT: Either this field or the job config's `query` field MUST be set in order for a job to be valid.

Job Creation Response JobCreateResponse

application/json

Response body returned on the successful creation of a new BLAST query job.

Inherits: object

Parameter

Type

Description

queryJobID* Query Job ID

string

Pattern: ^[\dA-Fa-f]{32}$

Min. length: 32

Max. length: 32

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Conflict ConflictError

application/json

The request could not be completed due to a conflict with the current state of the resource.

If you submitted a resource, that resource may already exist.

Inherits: string

Unprocessable Entity UnprocessableEntityError

application/json

The request payload or parameters are correctly structured but fail resource specific validation.

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
errors*	object	Additional properties: Yes
errors.general*	array	Non-field specific errors.
errors.general[]	string
errors.byKey*	object	Field specific errors Additional properties: Yes
errors.byKey.//*	array
errors.byKey.//[]	string

Response Body

{
  "status": "invalid-input",
  "message": "JSON validation failed",
  "errors": {
    "general": [],
    "byKey": {
      "id": [
        "Given ID value does not point to an existing record."
      ]
    }
  }
}

Returns details about the target job.

As a side effect, interactions with this endpoint will cause the target job to be added to the requesting user's job collection if it was not already present in that user's collection. This default behavior can be defeated by setting the save_job query parameter to false.

The reason this is done is to maintain a legacy job sharing behavior where a job is "shared with" a user automatically when they follow a link to that job.

Parameters

Parameter	Type	Description
Path
job-id*	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
Query
save_job Save Job	boolean	Flag that specifies whether the requested job should be saved to the user's job collection. To maintain legacy job sharing behavior, this parameter defaults to `true`. Default value: true

curl -X GET \
  undefined/jobs/{job-id}?save_job=<value>

Inherits: object

Parameter	Type	Description
queryJobID* Query Job ID	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
status* Job Status	string	Enum: queued in-progress complete failed expired Inherits: lib.JobStatus
jobConfig* Job Config	object	Job Configuration. Inherits: object
jobConfig.site* Target Site	string	Enum: AmoebaDB CryptoDB FungiDB GiardiaDB HostDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.TargetSite
jobConfig.targets* Query Targets	array
jobConfig.targets[]	object	Inherits: lib.QueryJobTarget
jobConfig.targets[].targetDisplayName*	string	Blast target display name, e.g. organism name.
jobConfig.targets[].targetFile*	string	Target blast database file.
jobConfig.query Blast Query	string	For Requests Inline query definition. This field is to be used for non-file-upload blast queries. If this field is not set, a query file must be uploaded for the request to be valid. For Responses This field will be omitted.
jobConfig.addToUserCollection Add to Collection	boolean	Adds this job to the users collection of jobs. The user's collection of jobs is what is returned by the `/jobs` endpoint.
blastConfig* Blast Tool Config	object	Blast Tool Configuration. Implemented by one of: BlastNConfig BlastPConfig BlastXConfig DeltaBlastConfig PSIBlastConfig RPSBlastConfig RPSTBlastNConfig TBlastNConfig TBlastXConfig Discriminator: tool Inherits: lib.BlastQueryConfig
blastConfig.tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
blastConfig.queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
blastConfig.queryLocation.start*	integer	Format: long
blastConfig.queryLocation.stop*	integer	Format: long
blastConfig.eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
blastConfig.softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
blastConfig.lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
blastConfig.queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
createdOn* Created On	datetime	Job creation timestamp.
userMeta User Metadata	object	Inherits: object
userMeta.summary Brief Summary	string	Brief, user defined summary or tagline for the job. Max. length: 512
userMeta.description Long Description	string	Longform, user provided description of the job.
subJobs Sub-Job IDs	array	List of IDs of sub-jobs that belong to this job.
subJobs[]	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Causes the target job to be restarted (if it is expired).

Parameters

Parameter	Type	Description
job-id*	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32

Parameter

Type

Description

Path

job-id*

string

Pattern: ^[\dA-Fa-f]{32}$

Min. length: 32

Max. length: 32

curl -X POST \
  undefined/jobs/{job-id}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Gone GoneError

application/json

The request could not be completed due to the requested resource or its underlying data no longer being present on the server.

Inherits: string

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Updates a user's job.

Parameters

Parameter	Type	Description
job-id*	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32

Parameter

Type

Description

Path

job-id*

string

Pattern: ^[\dA-Fa-f]{32}$

Min. length: 32

Max. length: 32

curl -X PATCH \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/jobs/{job-id}

Inherits: object

Parameter	Type	Description
userMeta User Metadata	object	Inherits: lib.QueryJobUserMeta
userMeta.summary Brief Summary	string	Brief, user defined summary or tagline for the job. Max. length: 512
userMeta.description Long Description	string	Longform, user provided description of the job.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Unprocessable Entity UnprocessableEntityError

application/json

The request payload or parameters are correctly structured but fail resource specific validation.

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
errors*	object	Additional properties: Yes
errors.general*	array	Non-field specific errors.
errors.general[]	string
errors.byKey*	object	Field specific errors Additional properties: Yes
errors.byKey.//*	array
errors.byKey.//[]	string

Response Body

{
  "status": "invalid-input",
  "message": "JSON validation failed",
  "errors": {
    "general": [],
    "byKey": {
      "id": [
        "Given ID value does not point to an existing record."
      ]
    }
  }
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Deletes the target job from the user's job collection.

Parameters

Parameter	Type	Description
job-id*	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32

Parameter

Type

Description

Path

job-id*

string

Pattern: ^[\dA-Fa-f]{32}$

Min. length: 32

Max. length: 32

curl -X DELETE \
  undefined/jobs/{job-id}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Returns the query for the target job, optionally as a download.

Parameters

Parameter	Type	Description
Path
job-id*	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
Query
download* Download	boolean	If set to true, the server will send a `Content-Disposition` header in the response indicating that the query file should be downloaded rather than rendered.

curl -X GET \
  undefined/jobs/{job-id}/query?download=<value>

Parameter	Type	Description
Content-Disposition	string	Present if the `download` query param was sent in with the request.

Job Query

text/plain

Raw query text

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Downloads the ASN1 result from the blast query execution.

Parameters

Parameter	Type	Description
Path
job-id*	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
Query
download* Download	boolean	If set to true, the server will send a `Content-Disposition` header in the response indicating that the result file should be downloaded rather than rendered.

curl -X GET \
  undefined/jobs/{job-id}/result?download=<value>

Parameter	Type	Description
Content-Disposition*	string	Sent to indicate the result is to be downloaded rather than rendered in the browser.

Job Result

text/plain

Raw job result.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Returns the stderr output for the blast tool execution for this job.

This output may be empty.

Parameters

Parameter	Type	Description
Path
job-id Query Job ID	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
Query
download Download	boolean	When set to true, indicates that the service should mark the returned file as an attachment using the `Content-Disposition` header to cause the file to be downloaded by the browser rather than rendered.

curl -X GET \
  undefined/jobs/{job-id}/stderr?download=<value>

Parameter	Type	Description
Content-Disposition	string	Present if the `download` query parameter was sent in with the request.

Response Body

FASTA-Reader: Ignoring invalid residues at position(s): On line 1: 1, 62-63
FASTA-Reader: Ignoring invalid residues at position(s): On line 2: 44-46
FASTA-Reader: Ignoring invalid residues at position(s): On line 3: 27-29
FASTA-Reader: Ignoring invalid residues at position(s): On line 4: 10-12, 73-75
FASTA-Reader: Ignoring invalid residues at position(s): On line 5: 56-58
FASTA-Reader: Ignoring invalid residues at position(s): On line 6: 39-41

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Lookup the statuses for the list of job IDs posted.

The response will be a mapping whose keys are the posted job IDs and whose values are the status of the job represented by the associated ID.

If a job ID in the input list does not appear to be a real/valid job ID, the ID will be omitted from the response object.

Each status value will be a valid JobStatus enum item, meaning they will each be one of:

"queued"
"in-progress"
"complete"
"failed"
"expired"

curl -X POST \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/statuses

Parameter	Type	Description
[]	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32

Parameter

Type

Description

[]

string

Pattern: ^[\dA-Fa-f]{32}$

Min. length: 32

Max. length: 32

Request Body

[
  "dd6060e5367622e574ffb38f32bfa049",
  "77542f92d9e68ea80eff4852ecc41fa4",
  "29e07b0b80181222ad33cbc8f679d672",
  "748ba381dd81bb8de615319837ffa350",
  "f4757ea84c455b04a1d307d4ac33049d"
]

Bulk Job Status Response JobBulkStatusResponse

application/json

Returns a mapping of job-id to status for each of the valid job IDs that appeared in the original bulk status request.

Additional properties: Yes

Inherits: object

Parameter	Type	Description
/^[\dA-Fa-f]{32}$/*	string	Enum: queued in-progress complete failed expired Inherits: lib.JobStatus

Response Body

{
  "dd6060e5367622e574ffb38f32bfa049": "queued",
  "29e07b0b80181222ad33cbc8f679d672": "complete",
  "748ba381dd81bb8de615319837ffa350": "in-progress",
  "f4757ea84c455b04a1d307d4ac33049d": "expired"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Retrieves an index of all the available blast targets.

curl -X GET \
  undefined/targets

Additional properties: Yes

Inherits: object

Parameter	Type	Description
/^\w+$/*	object	Additional properties: Yes Inherits: lib.BlastTargetMap
/^\w+$/./^\w+$/*	object	Inherits: lib.BlastableTarget
/^\w+$/./^\w+$/.naTargets	array	Default value: []
/^\w+$/./^\w+$/.naTargets[]	string
/^\w+$/./^\w+$/.aaTargets	array	Default value: []
/^\w+$/./^\w+$/.aaTargets[]	string

Response Body

{
  "PlasmoDB": {
    "Pberghei": {
      "naTargets": [
        "PbergheiESTs"
      ]
    },
    "PfalciparumGB4": {
      "naTargets": [
        "PfalciparumGB4AnnotatedCDSs",
        "PfalciparumGB4AnnotatedTranscripts",
        "PfalciparumGB4Genome"
      ],
      "aaTargets": [
        "PfalciparumGB4AnnotatedProteins"
      ]
    }
  }
}

A request to transfer ownership of jobs from a guest user to a logged in user, linking the logged in user to the jobs they created before they logged in.

curl -X POST \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/link-guest

Guest to User Job Transfer Request GuestJobTransferRequest

application/json

Request body for a request to transfer ownership of jobs from a guest user to a logged in user.

Inherits: object

Parameter	Type	Description
guestID* Guest ID	integer	ID assigned to the user before they were logged in. Format: int64

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Deletes all jobs in the job cache. This endpoint is to be used during site releases to clear any old data that may have been invalidated by the changes to the underlying site data.

Headers

Parameter	Type	Description
Admin-Token*	string

curl -X DELETE \
  -H "Admin-Token: <value>" \
  undefined/maintenance/cache

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Parameters

Parameter

Type

Description

Path

job-id Job ID

string

Pattern: ^[\dA-Fa-f]{32}$

Min. length: 32

Max. length: 32

Headers

Parameter	Type	Description
Admin-Token*	string

curl -X DELETE \
  -H "Admin-Token: <value>" \
  undefined/maintenance/cache/{job-id}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Lists job IDs for jobs owned by the current campus that are in the "failed" status.

Headers

Parameter	Type	Description
Admin-Token*	string

curl -X GET \
  -H "Admin-Token: <value>" \
  undefined/maintenance/broken-jobs

Parameter	Type	Description
[]	object	Inherits: object
[].queryJobID* Query Job ID	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
[].rawConfig*	any
[].createdOn* Created On	datetime	Job creation timestamp.
[].failedOn* Failed On	datetime	Job failure timestamp.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Renders the API documentation for this service.

curl -X GET \
  undefined/api

Prints information about the overall service health.

curl -X GET \
  undefined/health

HealthResponse HealthResponse

application/json

Health details about the service

Inherits: object

Parameter	Type	Description
status*	string	Status describes the overall service state. A status of "healthy" indicates that everything is running smoothly and all service dependencies are reachable and online. A status of "unhealthy" indicates that something is wrong with either this service or one or more of it's dependency services. Enum: healthy unhealthy
dependencies*	array	A list of external services that this service depends on and some details about them.
dependencies[]	object	Inherits: DependencyStatus
dependencies[].name*	string	Name of the external depdendency.
dependencies[].reachable*	boolean	Whether or not the external service is reachable.
dependencies[].online*	string	Whether or not the external service is online and available for requests. Enum: yes unknown no
info*	object	Additional properties: Yes
info.threads*	integer	Min. value: 1
info.uptime*	string
info.uptimeMillis*	integer	Min. value: 1 Format: int64

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Prometheus metrics for the service.

curl -X GET \
  undefined/metrics

Security Schemes

Types

Request body for a request to transfer ownership of jobs from a guest user to a logged in user.

Inherits: object

Model

Parameter	Type	Description
guestID* Guest ID	integer	ID assigned to the user before they were logged in. Format: int64

Inherits: object

Model

Parameter	Type	Description
jobConfig* Job Config	object	Job Configuration. Inherits: lib.QueryJobConfig
jobConfig.site* Target Site	string	Enum: AmoebaDB CryptoDB FungiDB GiardiaDB HostDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.TargetSite
jobConfig.targets* Query Targets	array
jobConfig.targets[]	object	Inherits: lib.QueryJobTarget
jobConfig.targets[].targetDisplayName*	string	Blast target display name, e.g. organism name.
jobConfig.targets[].targetFile*	string	Target blast database file.
jobConfig.query Blast Query	string	For Requests Inline query definition. This field is to be used for non-file-upload blast queries. If this field is not set, a query file must be uploaded for the request to be valid. For Responses This field will be omitted.
jobConfig.addToUserCollection Add to Collection	boolean	Adds this job to the users collection of jobs. The user's collection of jobs is what is returned by the `/jobs` endpoint.
blastConfig* Blast Tool Config	object	Blast Tool Configuration. Implemented by one of: BlastNConfig BlastPConfig BlastXConfig DeltaBlastConfig PSIBlastConfig RPSBlastConfig RPSTBlastNConfig TBlastNConfig TBlastXConfig Discriminator: tool Inherits: lib.BlastQueryConfig
blastConfig.tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
blastConfig.queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
blastConfig.queryLocation.start*	integer	Format: long
blastConfig.queryLocation.stop*	integer	Format: long
blastConfig.eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
blastConfig.softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
blastConfig.lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
blastConfig.queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
userMeta User Metadata	object	Inherits: lib.QueryJobUserMeta
userMeta.summary Brief Summary	string	Brief, user defined summary or tagline for the job. Max. length: 512
userMeta.description Long Description	string	Longform, user provided description of the job.

Inherits: object

Model

Parameter	Type	Description
userMeta User Metadata	object	Inherits: lib.QueryJobUserMeta
userMeta.summary Brief Summary	string	Brief, user defined summary or tagline for the job. Max. length: 512
userMeta.description Long Description	string	Longform, user provided description of the job.

Inherits: object

Model

Parameter	Type	Description
site* Target Site	string	Enum: AmoebaDB CryptoDB FungiDB GiardiaDB HostDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.TargetSite
targets* Query Targets	array
targets[]	object	Inherits: lib.QueryJobTarget
targets[].targetDisplayName*	string	Blast target display name, e.g. organism name.
targets[].targetFile*	string	Target blast database file.
query Blast Query	string	For Requests Inline query definition. This field is to be used for non-file-upload blast queries. If this field is not set, a query file must be uploaded for the request to be valid. For Responses This field will be omitted.
addToUserCollection Add to Collection	boolean	Adds this job to the users collection of jobs. The user's collection of jobs is what is returned by the `/jobs` endpoint.

Inherits: object

Model

Parameter	Type	Description
summary Brief Summary	string	Brief, user defined summary or tagline for the job. Max. length: 512
description Long Description	string	Longform, user provided description of the job.

Inherits: object

Model

Parameter	Type	Description
targetDisplayName*	string	Blast target display name, e.g. organism name.
targetFile*	string	Target blast database file.

Inherits: object

Model

Parameter	Type	Description
queryJobID* Query Job ID	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
status* Job Status	string	Enum: queued in-progress complete failed expired Inherits: lib.JobStatus
site* Target Site	string	Enum: AmoebaDB CryptoDB FungiDB GiardiaDB HostDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.TargetSite
createdOn* Created On	datetime	Job creation timestamp.
userMeta User Metadata	object	Inherits: object
userMeta.summary Brief Summary	string	Brief, user defined summary or tagline for the job. Max. length: 512
userMeta.description Long Description	string	Longform, user provided description of the job.

Inherits: object

Model

Parameter	Type	Description
queryJobID* Query Job ID	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
status* Job Status	string	Enum: queued in-progress complete failed expired Inherits: lib.JobStatus
jobConfig* Job Config	object	Job Configuration. Inherits: object
jobConfig.site* Target Site	string	Enum: AmoebaDB CryptoDB FungiDB GiardiaDB HostDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.TargetSite
jobConfig.targets* Query Targets	array
jobConfig.targets[]	object	Inherits: lib.QueryJobTarget
jobConfig.targets[].targetDisplayName*	string	Blast target display name, e.g. organism name.
jobConfig.targets[].targetFile*	string	Target blast database file.
jobConfig.query Blast Query	string	For Requests Inline query definition. This field is to be used for non-file-upload blast queries. If this field is not set, a query file must be uploaded for the request to be valid. For Responses This field will be omitted.
jobConfig.addToUserCollection Add to Collection	boolean	Adds this job to the users collection of jobs. The user's collection of jobs is what is returned by the `/jobs` endpoint.
blastConfig* Blast Tool Config	object	Blast Tool Configuration. Implemented by one of: BlastNConfig BlastPConfig BlastXConfig DeltaBlastConfig PSIBlastConfig RPSBlastConfig RPSTBlastNConfig TBlastNConfig TBlastXConfig Discriminator: tool Inherits: lib.BlastQueryConfig
blastConfig.tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
blastConfig.queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
blastConfig.queryLocation.start*	integer	Format: long
blastConfig.queryLocation.stop*	integer	Format: long
blastConfig.eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
blastConfig.softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
blastConfig.lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
blastConfig.queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
createdOn* Created On	datetime	Job creation timestamp.
userMeta User Metadata	object	Inherits: object
userMeta.summary Brief Summary	string	Brief, user defined summary or tagline for the job. Max. length: 512
userMeta.description Long Description	string	Longform, user provided description of the job.
subJobs Sub-Job IDs	array	List of IDs of sub-jobs that belong to this job.
subJobs[]	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32

Returns a mapping of job-id to status for each of the valid job IDs that appeared in the original bulk status request.

Additional properties: Yes

Inherits: object

Model

Parameter	Type	Description
/^[\dA-Fa-f]{32}$/*	string	Enum: queued in-progress complete failed expired Inherits: lib.JobStatus

Response body returned on the successful creation of a new BLAST query job.

Inherits: object

Model

Parameter

Type

Description

queryJobID* Query Job ID

string

Pattern: ^[\dA-Fa-f]{32}$

Min. length: 32

Max. length: 32

Enum:

queued
in-progress
complete
failed
expired

Inherits: string

Enum:

AmoebaDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: string

Additional properties: Yes

Inherits: object

Model

Parameter	Type	Description
/^\w+$/*	object	Additional properties: Yes Inherits: lib.BlastTargetMap
/^\w+$/./^\w+$/*	object	Inherits: lib.BlastableTarget
/^\w+$/./^\w+$/.naTargets	array	Default value: []
/^\w+$/./^\w+$/.naTargets[]	string
/^\w+$/./^\w+$/.aaTargets	array	Default value: []
/^\w+$/./^\w+$/.aaTargets[]	string

Additional properties: Yes

Inherits: object

Model

Parameter	Type	Description
/^\w+$/*	object	Inherits: lib.BlastableTarget
/^\w+$/.naTargets	array	Default value: []
/^\w+$/.naTargets[]	string
/^\w+$/.aaTargets	array	Default value: []
/^\w+$/.aaTargets[]	string

Inherits: object

Model

Parameter	Type	Description
naTargets	array	Default value: []
naTargets[]	string
aaTargets	array	Default value: []
aaTargets[]	string

Inherits: object

Model

Parameter	Type	Description
queryJobID* Query Job ID	string	Pattern: ^[\dA-Fa-f]{32}$ Min. length: 32 Max. length: 32
rawConfig*	any
createdOn* Created On	datetime	Job creation timestamp.
failedOn* Failed On	datetime	Job failure timestamp.

Discriminator: tool

Inherits: object

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double

Inherits: object

Model

Parameter	Type	Description
enabled Enable SEG	boolean	Whether SEG should be enabled.
window Window	integer	SEG window. Format: int Default value: 12
locut Locut	number	SEG locut. Format: double Default value: 2.2
hicut Hicut	number	SEG hicut. Format: double Default value: 2.5

Enum:

blastn
blastp
blastx
deltablast
psiblast
rpsblast
rpstblastn
tblastn
tblastx

Inherits: string

Translation Gen Code

Valid values are:

1, 2, 3, 4, 5, 6
9, 10, 11, 12, 13, 14, 15, 16
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31
33

This type should be an enum, however the code generated from the RAML when it is an enum is broken.

Min. value: 1

Max. value: 33

Format: int8

Inherits: integer

Inherits: object

Model

Parameter	Type	Description
start*	integer	Format: long
stop*	integer	Format: long

Enum:

both
minus
plus

Inherits: string

Discriminator: tool

Discriminator value: blastn

Inherits: lib.BlastQueryConfig

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
strand Strand	string	Query strand(s) to search against database/subject. Default value: "both" Enum: both minus plus Inherits: string
task Task	string	Task to execute. Default value: "megablast" Enum: blastn blastn-short dc-megablast megablast rmblastn Inherits: lib.BlastNTask
wordSize Word Size	integer	Word size for wordfinder algorithm (length of best perfect match). Min. value: 4 Format: int
gapOpen Gap Open	integer	Cost to open a gap. Format: int
gapExtend Gap Extend	integer	Cost to extend a gap. Format: int
penalty Penalty	integer	Penalty for a nucleotide mismatch. Format: int
reward Reward	integer	Reward for a nucleotide match. Format: int
useIndex Use Index	boolean	Use MegaBLAST database index.
indexName Index Name	string	MegaBLAST database index name (deprecated; use only for old style indices). Min. length: 1
dust DUST	object	Filter query sequence with DUST. Default value: {"level":20,"window":64,"linker":1} Inherits: lib.BlastNDust
dust.enabled Enable DUST	boolean	Whether DUST should be enabled. Default value: true
dust.level Level	integer	Score threshold for subwindows. Format: int Default value: 20
dust.window Window	integer	Window length. Format: int Default value: 64
dust.linker Linker	integer	How close masked intervals should be to get merged together. Format: int Default value: 1
dbSoftMask DB Soft Masking	string	Filtering algorithm ID to apply to the BLAST database as soft masking Incompatible with: `dbHardMask`
dbHardMask DB Hard Masking	string	Filtering algorithm ID to apply to the BLAST database as hard masking Incompatible with: `dbSoftMask`
percentIdentity Percent Identity	number	Percent identity. Max. value: 100 Format: double
cullingLimit Culling Limit	integer	If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit Incompatible with: `bestHitOverhang` `bestHitScoreEdge` Format: int
bestHitOverhang Best Hit Overhang	number	Best Hit algorithm overhang value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
bestHitScoreEdge Best Hit Score Edge	number	Best Hit algorithm score edge value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
subjectBestHit Subject Best Hit	boolean	Turn on best hit per subject sequence.
templateType Template Type	string	Discontiguous MegaBLAST template type. Requires: `templateLength` Enum: coding coding-and-optimal optimal Inherits: lib.BlastNTemplateType
templateLength Template Length	integer	Discontiguous MegaBLAST template length. Requires: `templateType` Format: int Enum: 16 18 21 Inherits: lib.BlastNTemplateLength
sumStats Use Sum Stats	boolean	Use sum statistics.
xDropoffPrelimGapped Preliminary Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for preliminary gapped extensions. Format: double
xDropoffFinalGapped Final Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for final gapped alignment. Format: double
nonGreedy Non Greedy Extension	boolean	Use non-greedy dynamic programming extension.
minRawGappedScore Minimum Raw Gapped Score	integer	Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stages Format: int
ungappedOnly Ungapped Alignment Only	boolean	Perform ungapped alignment only?
offDiagonalRange Off-Diagonal Range	integer	Number of off-diagonals to search for the 2nd hit, use 0 to turn off. Format: int

Enum:

blastn
blastn-short
dc-megablast
megablast
rmblastn

Inherits: string

Inherits: object

Model

Parameter	Type	Description
enabled Enable DUST	boolean	Whether DUST should be enabled. Default value: true
level Level	integer	Score threshold for subwindows. Format: int Default value: 20
window Window	integer	Window length. Format: int Default value: 64
linker Linker	integer	How close masked intervals should be to get merged together. Format: int Default value: 1

Enum:

coding
coding-and-optimal
optimal

Inherits: string

Format: int

Enum:

Inherits: integer

Discriminator: tool

Discriminator value: blastp

Inherits: lib.BlastQueryConfig

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
task Task	string	Task to execute. Default value: "blastp" Enum: blastp blastp-fast blastp-short Inherits: lib.BlastPTask
wordSize Word Size	integer	Word size for wordfinder algorithm (length of best perfect match). Min. value: 2 Format: int
gapOpen Gap Open	integer	Cost to open a gap. Format: int
gapExtend Gap Extend	integer	Cost to extend a gap. Format: int
matrix Scoring Matrix	string	Scoring matrix name (normally BLOSUM62) Enum: BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM90 PAM30 PAM70 PAM250 IDENTITY Inherits: lib.BlastPMatrix
threshold Minimum Word Score Threshold	number	Minimum word score such that the word is added to the BLAST lookup table. Format: double
compBasedStats Composition Based Statistics	string	Use composition-based statistics: No composition-based statistics Composition-based statistics as in NAR 29:2994-3005, 2001 Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Default value: "comp-based-score-adjustment-conditional" Enum: none comp-based-stats comp-based-score-adjustment-conditional comp-based-score-adjustment-unconditional Inherits: lib.BlastPCompBasedStats
seg SEG	object	Filter query sequence with SEG. Inherits: object
seg.enabled Enable SEG	boolean	Whether SEG should be enabled.
seg.window Window	integer	SEG window. Format: int Default value: 12
seg.locut Locut	number	SEG locut. Format: double Default value: 2.2
seg.hicut Hicut	number	SEG hicut. Format: double Default value: 2.5
dbSoftMask DB Soft Masking	string	Filtering algorithm ID to apply to the BLAST database as soft masking Incompatible with: `dbHardMask`
dbHardMask DB Hard Masking	string	Filtering algorithm ID to apply to the BLAST database as hard masking Incompatible with: `dbSoftMask`
cullingLimit Culling Limit	integer	If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit Incompatible with: `bestHitOverhang` `bestHitScoreEdge` Format: int
bestHitOverhang Best Hit Overhang	number	Best Hit algorithm overhang value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
bestHitScoreEdge Best Hit Score Edge	number	Best Hit algorithm score edge value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
subjectBestHit Subject Best Hit	boolean	Turn on best hit per subject sequence.
xDropoffPrelimGapped Preliminary Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for preliminary gapped extensions. Format: double
xDropoffFinalGapped Final Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for final gapped alignment. Format: double
ungappedOnly Ungapped Alignment Only	boolean	Perform ungapped alignment only?
useSWTraceback Use Smith-Waterman Traceback	boolean	Compute locally optimal Smith-Waterman alignments?

Enum:

none
comp-based-stats
comp-based-score-adjustment-conditional
comp-based-score-adjustment-unconditional

Inherits: string

Enum:

BLOSUM45
BLOSUM50
BLOSUM62
BLOSUM80
BLOSUM90
PAM30
PAM70
PAM250
IDENTITY

Inherits: string

Enum:

blastp
blastp-fast
blastp-short

Inherits: string

Discriminator: tool

Discriminator value: blastx

Inherits: lib.BlastQueryConfig

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
strand Strand	string	Query strand(s) to search against database/subject. Default value: "both" Enum: both minus plus Inherits: string
queryGenCode Translation Genetic Code	integer	Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes for details) Min. value: 1 Max. value: 33 Format: int8 Default value: 1 Inherits: integer
task Task	string	Task to execute. Default value: "blastx" Enum: blastx blastx-fast Inherits: lib.BlastXTask
wordSize Word Size	integer	Word size for wordfinder algorithm (length of best perfect match). Min. value: 2 Format: int
gapOpen Gap Open	integer	Cost to open a gap. Format: int
gapExtend Gap Extend	integer	Cost to extend a gap. Format: int
maxIntronLength Max Intron Length	integer	Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments Format: int
matrix Scoring Matrix	string	Scoring matrix name (normally BLOSUM62) Enum: BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM90 PAM30 PAM70 PAM250 Inherits: lib.BlastXMatrix
threshold Minimum Word Score Threshold	number	Minimum word score such that the word is added to the BLAST lookup table. Format: double
compBasedStats Composition Based Statistics	string	Use composition-based statistics: No composition-based statistics Composition-based statistics as in NAR 29:2994-3005, 2001 Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Default value: "comp-based-score-adjustment-conditional" Enum: none comp-based-stats comp-based-score-adjustment-conditional comp-based-score-adjustment-unconditional Inherits: lib.BlastXCompBasedStats
seg SEG	object	Filter query sequence with SEG. Default value: {"window":12,"locut":2.2,"hicut":2.5} Inherits: object
seg.enabled Enable SEG	boolean	Whether SEG should be enabled.
seg.window Window	integer	SEG window. Format: int Default value: 12
seg.locut Locut	number	SEG locut. Format: double Default value: 2.2
seg.hicut Hicut	number	SEG hicut. Format: double Default value: 2.5
dbSoftMask DB Soft Masking	string	Filtering algorithm ID to apply to the BLAST database as soft masking Incompatible with: `dbHardMask`
dbHardMask DB Hard Masking	string	Filtering algorithm ID to apply to the BLAST database as hard masking Incompatible with: `dbSoftMask`
cullingLimit Culling Limit	integer	If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit Incompatible with: `bestHitOverhang` `bestHitScoreEdge` Format: int
bestHitOverhang Best Hit Overhang	number	Best Hit algorithm overhang value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
bestHitScoreEdge Best Hit Score Edge	number	Best Hit algorithm score edge value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
subjectBestHit Subject Best Hit	boolean	Turn on best hit per subject sequence.
sumStats Use Sum Stats	boolean	Use sum statistics.
xDropoffPrelimGapped Preliminary Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for preliminary gapped extensions. Format: double
xDropoffFinalGapped Final Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for final gapped alignment. Format: double
ungappedOnly Ungapped Alignment Only	boolean	Perform ungapped alignment only?
useSWTraceback Use Smith-Waterman Traceback	boolean	Compute locally optimal Smith-Waterman alignments?

Enum:

blastx
blastx-fast

Inherits: string

Enum:

BLOSUM45
BLOSUM50
BLOSUM62
BLOSUM80
BLOSUM90
PAM30
PAM70
PAM250

Inherits: string

Enum:

none
comp-based-stats
comp-based-score-adjustment-conditional
comp-based-score-adjustment-unconditional

Inherits: string

Discriminator: tool

Discriminator value: deltablast

Inherits: lib.BlastQueryConfig

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
wordSize Word Size	integer	Word size for wordfinder algorithm (length of best perfect match). Min. value: 2 Format: int
gapOpen Gap Open	integer	Cost to open a gap. Format: int
gapExtend Gap Extend	integer	Cost to extend a gap. Format: int
matrix Scoring Matrix	string	Scoring matrix name (normally BLOSUM62) Enum: BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM90 PAM30 PAM70 PAM250 Inherits: lib.DeltaBlastMatrix
threshold Minimum Word Score Threshold	number	Minimum word score such that the word is added to the BLAST lookup table. Format: double
compBasedStats Composition Based Statistics	string	Use composition-based statistics: No composition-based statistics Composition-based statistics as in NAR 29:2994-3005, 2001 Default value: "comp-based-stats" Enum: none comp-based-stats Inherits: lib.DeltaBlastCompBasedStats
seg SEG	object	Filter query sequence with SEG. Inherits: object
seg.enabled Enable SEG	boolean	Whether SEG should be enabled.
seg.window Window	integer	SEG window. Format: int Default value: 12
seg.locut Locut	number	SEG locut. Format: double Default value: 2.2
seg.hicut Hicut	number	SEG hicut. Format: double Default value: 2.5
cullingLimit Culling Limit	integer	If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit Incompatible with: `bestHitOverhang` `bestHitScoreEdge` Format: int
bestHitOverhang Best Hit Overhang	number	Best Hit algorithm overhang value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
bestHitScoreEdge Best Hit Score Edge	number	Best Hit algorithm score edge value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
subjectBestHit Subject Best Hit	boolean	Turn on best hit per subject sequence.
sumStats Use Sum Stats	boolean	Use sum statistics.
xDropoffPrelimGapped Preliminary Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for preliminary gapped extensions. Format: double
xDropoffFinalGapped Final Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for final gapped alignment. Format: double
gapTrigger Gap Trigger	number	Number of bits to trigger gapping. Format: double Default value: 22
useSWTraceback Use Smith-Waterman Traceback	boolean	Compute locally optimal Smith-Waterman alignments?

Enum:

BLOSUM45
BLOSUM50
BLOSUM62
BLOSUM80
BLOSUM90
PAM30
PAM70
PAM250

Inherits: string

Enum:

none
comp-based-stats

Inherits: string

Discriminator: tool

Discriminator value: psiblast

Inherits: lib.BlastQueryConfig

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
wordSize Word Size	integer	Word size for wordfinder algorithm (length of best perfect match). Min. value: 2 Format: int
gapOpen Gap Open	integer	Cost to open a gap. Format: int
gapExtend Gap Extend	integer	Cost to extend a gap. Format: int
matrix Scoring Matrix	string	Scoring matrix name (normally BLOSUM62) Enum: BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM90 PAM30 PAM70 PAM250 Inherits: lib.PSIBlastMatrix
threshold Minimum Word Score Threshold	number	Minimum word score such that the word is added to the BLAST lookup table. Format: double
compBasedStats Composition Based Statistics	string	Use composition-based statistics: No composition-based statistics Composition-based statistics as in NAR 29:2994-3005, 2001 Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Default value: "comp-based-score-adjustment-conditional" Enum: none comp-based-stats comp-based-score-adjustment-conditional comp-based-score-adjustment-unconditional Inherits: lib.PSIBlastCompBasedStats
seg SEG	object	Filter query sequence with SEG. Inherits: object
seg.enabled Enable SEG	boolean	Whether SEG should be enabled.
seg.window Window	integer	SEG window. Format: int Default value: 12
seg.locut Locut	number	SEG locut. Format: double Default value: 2.2
seg.hicut Hicut	number	SEG hicut. Format: double Default value: 2.5
cullingLimit Culling Limit	integer	If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit Incompatible with: `bestHitOverhang` `bestHitScoreEdge` Format: int
bestHitOverhang Best Hit Overhang	number	Best Hit algorithm overhang value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
bestHitScoreEdge Best Hit Score Edge	number	Best Hit algorithm score edge value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
subjectBestHit Subject Best Hit	boolean	Turn on best hit per subject sequence.
sumStats Use Sum Stats	boolean	Use sum statistics.
xDropoffPrelimGapped Preliminary Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for preliminary gapped extensions. Format: double
xDropoffFinalGapped Final Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for final gapped alignment. Format: double
gapTrigger Gap Trigger	number	Number of bits to trigger gapping. Format: double Default value: 22
useSWTraceback Use Smith-Waterman Traceback	boolean	Compute locally optimal Smith-Waterman alignments?

Enum:

BLOSUM45
BLOSUM50
BLOSUM62
BLOSUM80
BLOSUM90
PAM30
PAM70
PAM250

Inherits: string

Enum:

none
comp-based-stats
comp-based-score-adjustment-conditional
comp-based-score-adjustment-unconditional

Inherits: string

Discriminator: tool

Discriminator value: rpsblast

Inherits: lib.BlastQueryConfig

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
compBasedStats Composition Based Statistics	string	Use composition-based statistics: No composition-based statistics Composition-based statistics as in NAR 29:2994-3005, 2001 Default value: "comp-based-stats" Enum: simplified comp-based-stats Inherits: lib.RPSBlastCompBasedStats
seg SEG	object	Filter query sequence with SEG. Inherits: object
seg.enabled Enable SEG	boolean	Whether SEG should be enabled.
seg.window Window	integer	SEG window. Format: int Default value: 12
seg.locut Locut	number	SEG locut. Format: double Default value: 2.2
seg.hicut Hicut	number	SEG hicut. Format: double Default value: 2.5
cullingLimit Culling Limit	integer	If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit Incompatible with: `bestHitOverhang` `bestHitScoreEdge` Format: int
bestHitOverhang Best Hit Overhang	number	Best Hit algorithm overhang value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
bestHitScoreEdge Best Hit Score Edge	number	Best Hit algorithm score edge value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
subjectBestHit Subject Best Hit	boolean	Turn on best hit per subject sequence.
sumStats Use Sum Stats	boolean	Use sum statistics.
xDropoffPrelimGapped Preliminary Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for preliminary gapped extensions. Format: double
xDropoffFinalGapped Final Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for final gapped alignment. Format: double
useSWTraceback Use Smith-Waterman Traceback	boolean	Compute locally optimal Smith-Waterman alignments?

Enum:

simplified
comp-based-stats

Inherits: string

Discriminator: tool

Discriminator value: rpstblastn

Inherits: lib.BlastQueryConfig

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
queryGenCode Translation Genetic Code	integer	Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes for details) Min. value: 1 Max. value: 33 Format: int8 Default value: 1 Inherits: integer
strand Strand	string	Query strand(s) to search against database/subject. Default value: "both" Enum: both minus plus Inherits: string
compBasedStats Composition Based Statistics	string	Use composition-based statistics: No composition-based statistics Composition-based statistics as in NAR 29:2994-3005, 2001 Default value: "comp-based-stats" Enum: none comp-based-stats Inherits: lib.RPSTBlastNCompBasedStats
seg SEG	object	Filter query sequence with SEG. Inherits: object
seg.enabled Enable SEG	boolean	Whether SEG should be enabled.
seg.window Window	integer	SEG window. Format: int Default value: 12
seg.locut Locut	number	SEG locut. Format: double Default value: 2.2
seg.hicut Hicut	number	SEG hicut. Format: double Default value: 2.5
sumStats Use Sum Stats	boolean	Use sum statistics.
xDropoffPrelimGapped Preliminary Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for preliminary gapped extensions. Format: double
xDropoffFinalGapped Final Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for final gapped alignment. Format: double
ungappedOnly Ungapped Alignment Only	boolean	Perform ungapped alignment only?
useSWTraceback Use Smith-Waterman Traceback	boolean	Compute locally optimal Smith-Waterman alignments?

Enum:

none
comp-based-stats

Inherits: string

Discriminator: tool

Discriminator value: tblastn

Inherits: lib.BlastQueryConfig

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
task Task	string	Task to execute. Default value: "tblastn" Enum: tblastn tblastn-fast Inherits: lib.TBlastNTask
wordSize Word Size	integer	Word size for wordfinder algorithm (length of best perfect match). Min. value: 2 Format: int
gapOpen Gap Open	integer	Cost to open a gap. Format: int
gapExtend Gap Extend	integer	Cost to extend a gap. Format: int
dbGenCode Translation Genetic Code	integer	Genetic code to use to translate database/subjects (see https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes for details) Min. value: 1 Max. value: 33 Format: int8 Default value: 1 Inherits: integer
maxIntronLength Max Intron Length	integer	Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments Format: int
matrix Scoring Matrix	string	Scoring matrix name (normally BLOSUM62) Enum: BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM90 PAM30 PAM70 PAM250 IDENTITY Inherits: lib.TBlastNMatrix
threshold Minimum Word Score Threshold	number	Minimum word score such that the word is added to the BLAST lookup table. Format: double
compBasedStats Composition Based Statistics	string	Use composition-based statistics: No composition-based statistics Composition-based statistics as in NAR 29:2994-3005, 2001 Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Default value: "comp-based-score-adjustment-conditional" Enum: none comp-based-stats comp-based-score-adjustment-conditional comp-based-score-adjustment-unconditional Inherits: lib.TBlastNCompBasedStats
seg SEG	object	Filter query sequence with SEG. Default value: {"window":12,"locut":2.2,"hicut":2.5} Inherits: object
seg.enabled Enable SEG	boolean	Whether SEG should be enabled.
seg.window Window	integer	SEG window. Format: int Default value: 12
seg.locut Locut	number	SEG locut. Format: double Default value: 2.2
seg.hicut Hicut	number	SEG hicut. Format: double Default value: 2.5
dbSoftMask DB Soft Masking	string	Filtering algorithm ID to apply to the BLAST database as soft masking Incompatible with: `dbHardMask`
dbHardMask DB Hard Masking	string	Filtering algorithm ID to apply to the BLAST database as hard masking Incompatible with: `dbSoftMask`
cullingLimit Culling Limit	integer	If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit Incompatible with: `bestHitOverhang` `bestHitScoreEdge` Format: int
bestHitOverhang Best Hit Overhang	number	Best Hit algorithm overhang value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
bestHitScoreEdge Best Hit Score Edge	number	Best Hit algorithm score edge value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
subjectBestHit Subject Best Hit	boolean	Turn on best hit per subject sequence.
sumStats Use Sum Stats	boolean	Use sum statistics.
xDropoffPrelimGapped Preliminary Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for preliminary gapped extensions. Format: double
xDropoffFinalGapped Final Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for final gapped alignment. Format: double
ungappedOnly Ungapped Alignment Only	boolean	Perform ungapped alignment only?
useSWTraceback Use Smith-Waterman Traceback	boolean	Compute locally optimal Smith-Waterman alignments?

Enum:

BLOSUM45
BLOSUM50
BLOSUM62
BLOSUM80
BLOSUM90
PAM30
PAM70
PAM250
IDENTITY

Inherits: string

Enum:

tblastn
tblastn-fast

Inherits: string

Enum:

none
comp-based-stats
comp-based-score-adjustment-conditional
comp-based-score-adjustment-unconditional

Inherits: string

Discriminator: tool

Discriminator value: tblastx

Inherits: lib.BlastQueryConfig

Model

Parameter	Type	Description
tool* Blast Tool	string	Target Blast+ query tool to execute. Enum: blastn blastp blastx deltablast psiblast rpsblast rpstblastn tblastn tblastx Inherits: lib.BlastQueryTool
queryLocation Query Location	object	Location on the query sequence in 1-based offsets. Inherits: lib.BlastLocation
queryLocation.start*	integer	Format: long
queryLocation.stop*	integer	Format: long
eValue Expectation Value	string	Expectation value (E) threshold for saving hits. Pattern: ^\d+(?:\.\d+)?(?:[eE]-?\d+)?$ Default value: "10"
softMasking Soft Masking	boolean	Apply filtering locations as soft masks.
lowercaseMasking Lowercase Masking	boolean	Use lower case filtering in query and subject sequence(s)?
queryCoverageHSPPercent Query Coverage HSP Percent	number	Percent query coverage per High Scoring Pair. Format: double
strand Strand	string	Query strand(s) to search against database/subject. Default value: "both" Enum: both minus plus Inherits: string
queryGenCode Translation Genetic Code	integer	Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes for details) Min. value: 1 Max. value: 33 Format: int8 Default value: 1 Inherits: integer
wordSize Word Size	integer	Word size for wordfinder algorithm (length of best perfect match). Min. value: 2 Format: int
maxIntronLength Max Intron Length	integer	Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments Format: int
matrix Scoring Matrix	string	Scoring matrix name (normally BLOSUM62) Enum: BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM90 PAM30 PAM70 PAM250 Inherits: lib.TBlastXMatrix
threshold Minimum Word Score Threshold	number	Minimum word score such that the word is added to the BLAST lookup table. Format: double
dbGenCode Translation Genetic Code	integer	Genetic code to use to translate database/subjects (see https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes for details) Min. value: 1 Max. value: 33 Format: int8 Default value: 1 Inherits: integer
seg SEG	object	Filter query sequence with SEG. Default value: {"window":12,"locut":2.2,"hicut":2.5} Inherits: object
seg.enabled Enable SEG	boolean	Whether SEG should be enabled.
seg.window Window	integer	SEG window. Format: int Default value: 12
seg.locut Locut	number	SEG locut. Format: double Default value: 2.2
seg.hicut Hicut	number	SEG hicut. Format: double Default value: 2.5
dbSoftMask DB Soft Masking	string	Filtering algorithm ID to apply to the BLAST database as soft masking Incompatible with: `dbHardMask`
dbHardMask DB Hard Masking	string	Filtering algorithm ID to apply to the BLAST database as hard masking Incompatible with: `dbSoftMask`
cullingLimit Culling Limit	integer	If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit Incompatible with: `bestHitOverhang` `bestHitScoreEdge` Format: int
bestHitOverhang Best Hit Overhang	number	Best Hit algorithm overhang value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
bestHitScoreEdge Best Hit Score Edge	number	Best Hit algorithm score edge value (recommended value: 0.1) Incompatible with: `cullingLimit` Min. value: 1e-15 Max. value: 0.499999999999999 Format: double
subjectBestHit Subject Best Hit	boolean	Turn on best hit per subject sequence.
sumStats Use Sum Stats	boolean	Use sum statistics.
xDropoffPrelimGapped Preliminary Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for preliminary gapped extensions. Format: double
xDropoffFinalGapped Final Gapped Extension X-Dropoff	number	X-dropoff value (in bits) for final gapped alignment. Format: double

Enum:

BLOSUM45
BLOSUM50
BLOSUM62
BLOSUM80
BLOSUM90
PAM30
PAM70
PAM250

Inherits: string

Discriminator: status

Inherits: object

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Enum:

bad-request
unauthorized
forbidden
not-found
bad-method
invalid-input
server-error

Inherits: string

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

The HTTP method used to request a resource is not allowed or configured by the server.

Discriminator: status

Discriminator value: bad-method

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "bad-method",
  "message": "PUT requests are not permitted on this endpoint"
}

The request could not be completed due to a conflict with the current state of the resource.

If you submitted a resource, that resource may already exist.

Inherits: string

The request could not be completed due to the requested resource or its underlying data no longer being present on the server.

Inherits: string

The request payload or parameters are correctly structured but fail resource specific validation.

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
errors*	object	Additional properties: Yes
errors.general*	array	Non-field specific errors.
errors.general[]	string
errors.byKey*	object	Field specific errors Additional properties: Yes
errors.byKey.//*	array
errors.byKey.//[]	string

Examples

{
  "status": "invalid-input",
  "message": "JSON validation failed",
  "errors": {
    "general": [],
    "byKey": {
      "id": [
        "Given ID value does not point to an existing record."
      ]
    }
  }
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Examples

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Health details about the service

Inherits: object

Model

Parameter	Type	Description
status*	string	Status describes the overall service state. A status of "healthy" indicates that everything is running smoothly and all service dependencies are reachable and online. A status of "unhealthy" indicates that something is wrong with either this service or one or more of it's dependency services. Enum: healthy unhealthy
dependencies*	array	A list of external services that this service depends on and some details about them.
dependencies[]	object	Inherits: DependencyStatus
dependencies[].name*	string	Name of the external depdendency.
dependencies[].reachable*	boolean	Whether or not the external service is reachable.
dependencies[].online*	string	Whether or not the external service is online and available for requests. Enum: yes unknown no
info*	object	Additional properties: Yes
info.threads*	integer	Min. value: 1
info.uptime*	string
info.uptimeMillis*	integer	Min. value: 1 Format: int64

Inherits: object

Model

Parameter	Type	Description
name*	string	Name of the external depdendency.
reachable*	boolean	Whether or not the external service is reachable.
online*	string	Whether or not the external service is online and available for requests. Enum: yes unknown no

MultiBlast Query Service v2.0.0

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422 Unprocessable Entity

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200 OK

401 Unauthorized

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500 Internal Server Error

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204 No Content

401 Unauthorized

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404 Not Found

410 Gone

500 Internal Server Error

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204 No Content

400 Bad Request

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422 Unprocessable Entity

500 Internal Server Error

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204 No Content

401 Unauthorized

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500 Internal Server Error

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200 OK

401 Unauthorized

404 Not Found

500 Internal Server Error

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200 OK

401 Unauthorized

403 Forbidden

404 Not Found

500 Internal Server Error

Parameters

200 OK

401 Unauthorized

403 Forbidden

404 Not Found

500 Internal Server Error

Request Body

200 OK