BLAST Sequence(s)

Protein databases

Advanced parameters:

-evalue <Real>
   Expectation value (E) threshold for saving hits
   Default = `10'
 -word_size <Integer, >=2>
   Word size for wordfinder algorithm
 -gapopen <Integer>
   Cost to open a gap
 -gapextend <Integer>
   Cost to extend a gap
 -matrix <String>
   Scoring matrix name (normally BLOSUM62)
 -threshold <Real, >=0>
   Minimum word score such that the word is added to the BLAST lookup table
 -comp_based_stats <String>
   Use composition-based statistics for blastp / tblastn:
       D or d: default (equivalent to 2)
       0 or F or f: no composition-based statistics
       1: Composition-based statistics as in NAR 29:2994-3005, 2001
       2 or T or t : Composition-based score adjustment as in Bioinformatics
   21:902-911,
       2005, conditioned on sequence properties
       3: Composition-based score adjustment as in Bioinformatics 21:902-911,
       2005, unconditionally
   For programs other than tblastn, must either be absent or be D, F or 0
   Default = `2'
 -num_descriptions <Integer, >=0>
   Number of database sequences to show one-line descriptions for
   Default = `500'
 -num_alignments <Integer, >=0>
   Number of database sequences to show alignments for
   Default = `250'
 *** Query filtering options
 -seg <String>
   Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
   'no' to disable)
   Default = `no'
 -soft_masking <Boolean>
   Apply filtering locations as soft masks
   Default = `false'
 -lcase_masking
   Use lower case filtering in query and subject sequence(s)?
 *** Restrict search or results
 -gilist <String>
   Restrict search of database to list of GI's
    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
   subject_loc
 -seqidlist <String>
   Restrict search of database to list of SeqId's
    * Incompatible with:  gilist, negative_gilist, remote, subject,
   subject_loc
 -negative_gilist <String>
   Restrict search of database to everything except the listed GIs
    * Incompatible with:  gilist, seqidlist, remote, subject, subject_loc
 -entrez_query <String>
   Restrict search with the given Entrez query
    * Requires:  remote
 -db_soft_mask <String>
   Filtering algorithm ID to apply to the BLAST database as soft masking
    * Incompatible with:  subject, subject_loc
 -culling_limit <Integer, >=0>
   If the query range of a hit is enveloped by that of at least this many
   higher-scoring hits, delete the hit
    * Incompatible with:  best_hit_overhang, best_hit_score_edge
 -best_hit_overhang <Real, (>0 and <0.5)>
   Best Hit algorithm overhang value (recommended value: 0.1)
    * Incompatible with:  culling_limit
 -best_hit_score_edge <Real, (>0 and <0.5)>
   Best Hit algorithm score edge value (recommended value: 0.1)
    * Incompatible with:  culling_limit
 -max_target_seqs <Integer, >=1>
   Maximum number of aligned sequences to keep 
  

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