Package org.veupathdb.lib.blast.psiblast.fields
See: Description
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Class Summary Class Description CompBasedStatsPSI -comp_based_stats <String>Use composition-based statistics:Dord: default (equivalent to 2)0orForf: No composition-based statistics1: Composition-based statistics as in NAR 29:2994-3005, 20012orTort: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
IgnoreMSAMaster -ignore_msa_masterIgnore the master sequence when creating PSSMRequires: -in_msa InMSAFile -in_msa <File_In>File name of multiple sequence alignment to restart PSI-BLASTMSAMasterIndex -msa_master_idx <Integer, >=1>Ordinal number (1-based index) of the sequence to use as a master in the multiple sequence alignment.MatrixPSI -matrix <String>Scoring matrix name (normally BLOSUM62)PHIPatternFile -phi_pattern <File_In>File name containing pattern to searchSoftMaskingPSI -soft_masking <Boolean>Apply filtering locations as soft masksDefault =falseWordSizePSI -word_size <Integer, >=2>Word size for wordfinder algorithm -
Enum Summary Enum Description CompBasedStatsPSIValue MatrixPSIType -
Object Summary Object Description Companion -
Interface Summary Interface Description SegPSI