Options

General Search Options
  • -task <String, Permissible values: 'tblastn' 'tblastn-fast'>
  Task to execute
  Default = 'tblastn'
  • -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
  • -db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
  Genetic code to use to translate database/subjects (see user manual for details)
  Default = '1' 
  • -max_intron_length <Integer, >=0>
  Length of the largest intron allowed in a translated nucleotide sequence when
   linking multiple distinct alignments
  Default = '0'
  • -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'

Formatting Options
  • -show_gis
  Show NCBI GIs in deflines?
  • -num_descriptions <Integer, >=0>
  Number of database sequences to show one-line descriptions for
  Not applicable for outfmt > 4
  Default = '500'
  * Incompatible with:  max_target_seqs
  •  -num_alignments <Integer, >=0>
  Number of database sequences to show alignments for
  Default = '250'
  * Incompatible with:  max_target_seqs

Query filtering options
  • -seg <String>
  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
  or 'no' to disable)
  Default = '12 2.2 2.5'
  • -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 GIs
  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -seqidlist <String>
  Restrict search of database to list of SeqIDs
  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_gilist <String>
  Restrict search of database to everything except the specified GIs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_seqidlist <String>
  Restrict search of database to everything except the specified SeqIDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -taxids <String>
  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxids <String>
  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
   subject_loc
  • -taxidlist <String>
  Restrict search of database to include only the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxidlist <String>
  Restrict search of database to everything except the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxids, 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:  db_hard_mask, subject, subject_loc
  • -db_hard_mask <String>
  Filtering algorithm ID to apply to the BLAST database as hard masking
  * Incompatible with:  db_soft_mask, subject, subject_loc
  • -qcov_hsp_perc <Real, 0..100>
  Percent query coverage per hsp
  • -max_hsps <Integer, >=1>
  Set maximum number of HSPs per subject sequence to save for each query
  • -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
  • -subject_besthit
  Turn on best hit per subject sequence
  • -max_target_seqs <Integer, >=1>
  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
  Default = '500'
  * Incompatible with:  num_descriptions, num_alignments

Statistical options
  • -dbsize <Int8>
  Effective length of the database
  • -searchsp <Int8, >=0>
  Effective length of the search space
  • -sum_stats <Boolean>
  Use sum statistics

Extension options
  • -xdrop_ungap <Real>
  X-dropoff value (in bits) for ungapped extensions
  • -xdrop_gap <Real>
  X-dropoff value (in bits) for preliminary gapped extensions
  • -xdrop_gap_final <Real>
  X-dropoff value (in bits) for final gapped alignment
  • -ungapped
  Perform ungapped alignment only?
  • -window_size <Integer, >=0>
  Multiple hits window size, use 0 to specify 1-hit algorithm
General Search Options
  • -task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast' 'megablast' 'rmblastn'>
  Task to execute
  Default = 'megablast'
  • -evalue <Real>
  Expectation value (E) threshold for saving hits
  Default = '10' (1000 for blastn-short)
  • -word_size <Integer, >=2>
  Word size for wordfinder algorithm (length of best perfect match)
  • -gapopen <Integer>
  Cost to open a gap
  • -gapextend <Integer>
  Cost to extend a gap
  • -penalty <Integer, <=0>
  Penalty for a nucleotide mismatch
  • -reward <Integer, >=0>
  Reward for a nucleotide match
  • -use_index <Boolean>
  Use MegaBLAST database index
  Default = 'false'

Formatting Options
  • -show_gis
  Show NCBI GIs in deflines?
  • -num_descriptions <Integer, >=0>
  Number of database sequences to show one-line descriptions for
  Not applicable for outfmt > 4
  Default = '500'
  * Incompatible with:  max_target_seqs
  •  -num_alignments <Integer, >=0>
  Number of database sequences to show alignments for
  Default = '250'
  * Incompatible with:  max_target_seqs
  •  -line_length <Integer, >=1>
  Line length for formatting alignments
  Not applicable for outfmt > 4
  Default = '60'

Query filtering options
  • -dust <String>
  Filter query sequence with DUST (Format: 'yes', 'level window linker', or
   'no' to disable)
  Default = '20 64 1' ('no' for blastn-short)
  • -soft_masking <Boolean>
  Apply filtering locations as soft masks
  Default = 'true'
  • -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 GIs
  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -seqidlist <String>
  Restrict search of database to list of SeqIDs
  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_gilist <String>
  Restrict search of database to everything except the specified GIs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_seqidlist <String>
  Restrict search of database to everything except the specified SeqIDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -taxids <String>
  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxids <String>
  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
   subject_loc
  • -taxidlist <String>
  Restrict search of database to include only the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxidlist <String>
  Restrict search of database to everything except the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxids, 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:  db_hard_mask, subject, subject_loc
  • -db_hard_mask <String>
  Filtering algorithm ID to apply to the BLAST database as hard masking
  * Incompatible with:  db_soft_mask, subject, subject_loc
  • -perc_identity <Real, 0..100>
  Percent identity
  • -qcov_hsp_perc <Real, 0..100>
  Percent query coverage per hsp
  • -max_hsps <Integer, >=1>
  Set maximum number of HSPs per subject sequence to save for each query
  • -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
  • -subject_besthit
  Turn on best hit per subject sequence
  • -max_target_seqs <Integer, >=1>
  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
  Default = '500'
  * Incompatible with:  num_descriptions, num_alignments

Discontiguous MegaBLAST options
  • -template_type <String, `coding', `coding_and_optimal', `optimal'>
  Discontiguous MegaBLAST template type
  * Requires:  template_length
  • -template_length <Integer, Permissible values: '16' '18' '21' >
  Discontiguous MegaBLAST template length
  * Requires:  template_type

Statistical options
  • -dbsize <Int8>
  Effective length of the database
  • -searchsp <Int8, >=0>
  Effective length of the search space

Extension options
  • -xdrop_ungap <Real>
  X-dropoff value (in bits) for ungapped extensions
  • -xdrop_gap <Real>
  X-dropoff value (in bits) for preliminary gapped extensions
  • -xdrop_gap_final <Real>
  X-dropoff value (in bits) for final gapped alignment
  • -no_greedy
  Use non-greedy dynamic programming extension
  • -min_raw_gapped_score <Integer>
  Minimum raw gapped score to keep an alignment in the preliminary gapped and
   traceback stages
  • -ungapped
  Perform ungapped alignment only?
  • -window_size <Integer, >=0>
  Multiple hits window size, use 0 to specify 1-hit algorithm
  • -off_diagonal_range <Integer, >=0>
  Number of off-diagonals to search for the 2nd hit, use 0 to turn off
  Default = `0'

Miscellaneous options
  • -parse_deflines <Real>
  Should the query and subject defline(s) be parsed?
Input Query Options
  • -strand <String, `both', `minus', `plus'>
  Query strand(s) to search against database/subject
  Default = 'both'
  • -query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
  Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/
   taxonomyhome.html/index.cgi?chapter=cgencodes for details)
  Default = '1'

General Search Options
  • -task <String, Permissible values: 'blastx' 'blastx-fast'>
  Task to execute
  Default = 'blastx'
  • -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
  • -max_intron_length <Integer, >=0>
  Length of the largest intron allowed in a translated nucleotide sequence when
   linking multiple distinct alignments
  Default = '0'
  • -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:
      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
  Default = '2'

Formatting Options
  • -show_gis
  Show NCBI GIs in deflines?
  • -num_descriptions <Integer, >=0>
  Number of database sequences to show one-line descriptions for
  Not applicable for outfmt > 4
  Default = '500'
  * Incompatible with:  max_target_seqs
  •  -num_alignments <Integer, >=0>
  Number of database sequences to show alignments for
  Default = '250'
  * Incompatible with:  max_target_seqs
  •  -sorthits <Integer, (>=0 and =<4)>
  Sorting option for hits:
   alignment view options:
     0 = Sort by evalue,
     1 = Sort by bit score,
     2 = Sort by total score,
     3 = Sort by percent identity,
     4 = Sort by query coverage
   Not applicable for outfmt > 4
  •  -sorthsps <Integer, (>=0 and =<4)>
  Sorting option for hps:
     0 = Sort by hsp evalue,
     1 = Sort by hsp score,
     2 = Sort by hsp query start,
     3 = Sort by hsp percent identity,
     4 = Sort by hsp subject start
   Not applicable for outfmt != 0

Query filtering options
  • -seg <String>
  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
  or 'no' to disable)
  Default = '12 2.2 2.5'
  • -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 GIs
  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -seqidlist <String>
  Restrict search of database to list of SeqIDs
  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_gilist <String>
  Restrict search of database to everything except the specified GIs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_seqidlist <String>
  Restrict search of database to everything except the specified SeqIDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -taxids <String>
  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxids <String>
  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
   subject_loc
  • -taxidlist <String>
  Restrict search of database to include only the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxidlist <String>
  Restrict search of database to everything except the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
   subject_loc
  •  -ipglist <String>
  Restrict search of database to list of IPGs
  * Incompatible with:  subject, subject_loc
  •  -negative_ipglist <String>
  Restrict search of database to everything except the specified IPGs
  * Incompatible with:  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:  db_hard_mask, subject, subject_loc
  • -db_hard_mask <String>
  Filtering algorithm ID to apply to the BLAST database as hard masking
  * Incompatible with:  db_soft_mask, subject, subject_loc
  • -qcov_hsp_perc <Real, 0..100>
  Percent query coverage per hsp
  • -max_hsps <Integer, >=1>
  Set maximum number of HSPs per subject sequence to save for each query
  • -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
  • -subject_besthit
  Turn on best hit per subject sequence
  • -max_target_seqs <Integer, >=1>
  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
  Default = '500'
  * Incompatible with:  num_descriptions, num_alignments

Statistical options
  • -dbsize <Int8>
  Effective length of the database
  • -searchsp <Int8, >=0>
  Effective length of the search space
  • -sum_stats <Boolean>
  Use sum statistics

Extension options
  • -xdrop_ungap <Real>
  X-dropoff value (in bits) for ungapped extensions
  • -xdrop_gap <Real>
  X-dropoff value (in bits) for preliminary gapped extensions
  • -xdrop_gap_final <Real>
  X-dropoff value (in bits) for final gapped alignment
  • -window_size <Integer, >=0>
  Multiple hits window size, use 0 to specify 1-hit algorithm
  • -ungapped
  Perform ungapped alignment only?

Miscellaneous options
  • -parse_deflines <Real>
  Should the query and subject defline(s) be parsed?
  • -use_sw_tback <Real>
  Compute locally optimal Smith-Waterman alignments?
Input Query Options
  • -strand <String, `both', `minus', `plus'>
  Query strand(s) to search against database/subject
  Default = 'both'
  • -query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
  Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/
   taxonomyhome.html/index.cgi?chapter=cgencodes for details)
  Default = '1'

General Search Options
  • -evalue <Real>
  Expectation value (E) threshold for saving hits
  Default = '10'
  • -word_size <Integer, >=2>
  Word size for wordfinder algorithm
  • -max_intron_length <Integer, >=0>
  Length of the largest intron allowed in a translated nucleotide sequence when
   linking multiple distinct alignments
  Default = '0'
  • -matrix <String>
  Scoring matrix name (normally BLOSUM62)
  • -threshold <Real, >=0>
  Minimum word score such that the word is added to the BLAST lookup table
  • -db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
  Genetic code to use to translate database/subjects (see user manual for details)
  Default = '1'

Formatting Options
  • -show_gis
  Show NCBI GIs in deflines?
  • -num_descriptions <Integer, >=0>
  Number of database sequences to show one-line descriptions for
  Not applicable for outfmt > 4
  Default = '500'
  * Incompatible with:  max_target_seqs
  •  -num_alignments <Integer, >=0>
  Number of database sequences to show alignments for
  Default = '250'
  * Incompatible with:  max_target_seqs
  •  -sorthits <Integer, (>=0 and =<4)>
  Sorting option for hits:
   alignment view options:
     0 = Sort by evalue,
     1 = Sort by bit score,
     2 = Sort by total score,
     3 = Sort by percent identity,
     4 = Sort by query coverage
   Not applicable for outfmt > 4
  •  -sorthsps <Integer, (>=0 and =<4)>
  Sorting option for hps:
     0 = Sort by hsp evalue,
     1 = Sort by hsp score,
     2 = Sort by hsp query start,
     3 = Sort by hsp percent identity,
     4 = Sort by hsp subject start
   Not applicable for outfmt != 0

Query filtering options
  • -seg <String>
  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
  or 'no' to disable)
  Default = '12 2.2 2.5'
  • -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 GIs
  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -seqidlist <String>
  Restrict search of database to list of SeqIDs
  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_gilist <String>
  Restrict search of database to everything except the specified GIs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_seqidlist <String>
  Restrict search of database to everything except the specified SeqIDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -taxids <String>
  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxids <String>
  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
   subject_loc
  • -taxidlist <String>
  Restrict search of database to include only the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxidlist <String>
  Restrict search of database to everything except the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxids, 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:  db_hard_mask, subject, subject_loc
  • -db_hard_mask <String>
  Filtering algorithm ID to apply to the BLAST database as hard masking
  * Incompatible with:  db_soft_mask, subject, subject_loc
  • -qcov_hsp_perc <Real, 0..100>
  Percent query coverage per hsp
  • -max_hsps <Integer, >=1>
  Set maximum number of HSPs per subject sequence to save for each query
  • -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
  • -subject_besthit
  Turn on best hit per subject sequence
  • -max_target_seqs <Integer, >=1>
  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
  Default = '500'
  * Incompatible with:  num_descriptions, num_alignments

Statistical options
  • -dbsize <Int8>
  Effective length of the database
  • -searchsp <Int8, >=0>
  Effective length of the search space
  • -sum_stats <Boolean>
  Use sum statistics

Search Strategy options
  • -import_search_strategy <File_In>
  Search strategy to use
  * Incompatible with:  export_search_strategy
  • -export_search_strategy <File_Out>
  File name to record the search strategy used
  * Incompatible with:  import_search_strategy
  • -sum_stats <Boolean>
  Use sum statistics

Extension options
  • -xdrop_ungap <Real>
  X-dropoff value (in bits) for ungapped extensions
  • -window_size <Integer, >=0>
  Multiple hits window size, use 0 to specify 1-hit algorithm

Miscellaneous options
  • -parse_deflines <Real>
  Should the query and subject defline(s) be parsed?
General Search Options
  • -task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short'>
  Task to execute
  Default = 'blastp'
  • -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:
      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
  Default = '2'

Formatting Options
  • -num_descriptions <Integer, >=0>
  Number of database sequences to show one-line descriptions for
  Not applicable for outfmt > 4
  Default = '500'
  * Incompatible with:  max_target_seqs
  •  -num_alignments <Integer, >=0>
  Number of database sequences to show alignments for
  Default = '250'
  * Incompatible with:  max_target_seqs
  •  -sorthits <Integer, (>=0 and =<4)>
  Sorting option for hits:
   alignment view options:
     0 = Sort by evalue,
     1 = Sort by bit score,
     2 = Sort by total score,
     3 = Sort by percent identity,
     4 = Sort by query coverage
   Not applicable for outfmt > 4
  •  -sorthsps <Integer, (>=0 and =<4)>
  Sorting option for hps:
     0 = Sort by hsp evalue,
     1 = Sort by hsp score,
     2 = Sort by hsp query start,
     3 = Sort by hsp percent identity,
     4 = Sort by hsp subject start
   Not applicable for outfmt != 0

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 GIs
  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -seqidlist <String>
  Restrict search of database to list of SeqIDs
  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_gilist <String>
  Restrict search of database to everything except the specified GIs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_seqidlist <String>
  Restrict search of database to everything except the specified SeqIDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -taxids <String>
  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxids <String>
  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
   subject_loc
  • -taxidlist <String>
  Restrict search of database to include only the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
  • -negative_taxidlist <String>
  Restrict search of database to everything except the specified taxonomy IDs
  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
   subject_loc
  •  -ipglist <String>
  Restrict search of database to list of IPGs
  * Incompatible with:  subject, subject_loc
  •  -negative_ipglist <String>
  Restrict search of database to everything except the specified IPGs
  * Incompatible with:  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:  db_hard_mask, subject, subject_loc
  • -db_hard_mask <String>
  Filtering algorithm ID to apply to the BLAST database as hard masking
  * Incompatible with:  db_soft_mask, subject, subject_loc
  • -qcov_hsp_perc <Real, 0..100>
  Percent query coverage per hsp
  • -max_hsps <Integer, >=1>
  Set maximum number of HSPs per subject sequence to save for each query
  • -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
  • -subject_besthit
  Turn on best hit per subject sequence
  • -max_target_seqs <Integer, >=1>
  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
  Default = '500'
  * Incompatible with:  num_descriptions, num_alignments

Statistical options
  • -dbsize <Int8>
  Effective length of the database
  • -searchsp <Int8, >=0>
  Effective length of the search space

Extension options
  • -xdrop_ungap <Real>
  X-dropoff value (in bits) for ungapped extensions
  • -xdrop_gap <Real>
  X-dropoff value (in bits) for preliminary gapped extensions
  • -xdrop_gap_final <Real>
  X-dropoff value (in bits) for final gapped alignment
  • -window_size <Integer, >=0>
  Multiple hits window size, use 0 to specify 1-hit algorithm
  • -ungapped
  Perform ungapped alignment only?

Miscellaneous options
  • -parse_deflines <Real>
  Should the query and subject defline(s) be parsed?
  • -use_sw_tback <Real>
  Compute locally optimal Smith-Waterman alignments?

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