Package org.veupathdb.lib.blast.blastn.fields
See: Description
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Object Summary Object Description Companion -
Interface Summary Interface Description Dust -dust <String>Filter query sequence with DUST (Format: 'yes', 'level window linker', or 'no' to disable)Default ="20 64 1" -
Class Summary Class Description FilteringDB -filtering_db <String>BLAST database containing filtering elements (i.e.IndexName -index_name <String>MegaBLAST database index name (deprecated; use only for old style indices)MinRawGappedScore -min_raw_gapped_score <Integer>Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stagesNonGreedy -no_greedyUse non-greedy dynamic programming extension OffDiagonalRange -off_diagonal_range <Integer, >=0>Number of off-diagonals to search for the 2nd hit, use 0 to turn offDefault =0Penalty -penalty <Integer, <=0>Penalty for a nucleotide mismatchPercentIdentity -perc_identity <Real, 0..100>Percent identityReward -reward <Integer, >=0>Reward for a nucleotide matchSoftMaskingN -soft_masking <Boolean>Apply filtering locations as soft masksDefault =trueBlastNTask -task <String>Permissible values:'blastn'
'blastn-short'
'dc-megablast'
'megablast'
'rmblastn'
megablastTemplateLength -template_length <Integer>Permissible values:16
18
21
TemplateType -template_type <String>Permissible Values:coding
coding_and_optimal
optimal
UseIndex -use_index <Boolean>Use MegaBLAST database indexDefault =falseWindowMaskerDB -window_masker_db <String>Enable WindowMasker filtering using this repeats database.WindowMaskerTaxID -window_masker_taxid <Integer>Enable WindowMasker filtering using a Taxonomic ID -
Enum Summary Enum Description BlastNTaskType TemplateLengthValue TemplateTypeType