-task <String>
Task to execute for the selected BLAST algorithm
Options for BLASTN:
'blastn' Traditional BLASTN requiring an exact match of 11 (default)
'blastn-short' Optimized BLASTN for query sequences shorter than 50 nucleotides.
'megablast' Traditional megablast used to find very similar sequences (e.g., intraspecies or closely related species).
'dc-megablast' Discontiguous megablast used to find somewhat distant sequences (e.g., interspecies).
'rmblastn'
Options for BLASTP:
'blastp' Standard protein-protein comparisons (default)
'blastp-fast' Faster BLASTP searches using longer words for protein seeding
'blastp-short' Optimized BLASTP comparisons for query sequences shorter than 30 residues
Options for BLASTX:
'blastx' Standard nucleotide-protein comparisons (default)
'blastx-fast' Optimized nucleotide-protein comparisons
Options for TBLASTN:
'tblastn' Standard protein-nucleotide comparisons (default)
'tblastn-fast' Optimized protein-nucleotide comparisons
Not applicable for TBLASTX
-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'
-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)?
-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
-task <String>
Task to execute for the selected BLAST algorithm
Options for BLASTN:
'blastn' Traditional BLASTN requiring an exact match of 11 (default)
'blastn-short' Optimized BLASTN for query sequences shorter than 50 nucleotides.
'megablast' Traditional megablast used to find very similar sequences (e.g., intraspecies or closely related species).
'dc-megablast' Discontiguous megablast used to find somewhat distant sequences (e.g., interspecies).
'rmblastn'
Options for BLASTP:
'blastp' Standard protein-protein comparisons (default)
'blastp-fast' Faster BLASTP searches using longer words for protein seeding
'blastp-short' Optimized BLASTP comparisons for query sequences shorter than 30 residues
Options for BLASTX:
'blastx' Standard nucleotide-protein comparisons (default)
'blastx-fast' Optimized nucleotide-protein comparisons
Options for TBLASTN:
'tblastn' Standard protein-nucleotide comparisons (default)
'tblastn-fast' Optimized protein-nucleotide comparisons
Not applicable for TBLASTX
-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'
-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)?
-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