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?

If you use this service, please cite: Data: Bult CJ, Sternberg PW. 2023. The Alliance of Genome Resources: transforming comparative genomics. Mamm Genome, 2023;34(4):531-44. doi: 10.1007/s00335-023-10015-2. PMID: 37666946. BLAST service: Anurag Priyam, Ben J Woodcroft, Vivek Rai, Ismail Moghul, Alekhya Munagala, Filip Ter, Hiten Chowdhary, Iwo Pieniak, Lawrence J Maynard, Mark Anthony Gibbins, HongKee Moon, Austin Davis-Richardson, Mahmut Uludag, Nathan S Watson-Haigh, Richard Challis, Hiroyuki Nakamura, Emeline Favreau, Esteban A Gómez, Tomás Pluskal, Guy Leonard, Wolfgang Rumpf, Yannick Wurm. 2019. Sequenceserver: A modern graphical user interface for custom BLAST databases.Molecular Biology and Evolution 36(12):2922–2924, https://doi.org/10.1093/molbev/msz185. PMID: 31411700

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JBrowse genome browser links may not resolve correctly for every organism yet. The rest of the service is unaffected.

If you use this service, please cite

Data

Bult CJ, Sternberg PW.

The Alliance of Genome Resources: transforming comparative genomics.

Mamm Genome 2023;34(4):531–44.

doi:10.1007/s00335-023-10015-2 PMID 37666946

BLAST service

Priyam A, Woodcroft BJ, Rai V, et al.

Anurag Priyam, Ben J Woodcroft, Vivek Rai, Ismail Moghul, Alekhya Munagala, Filip Ter, Hiten Chowdhary, Iwo Pieniak, Lawrence J Maynard, Mark Anthony Gibbins, HongKee Moon, Austin Davis-Richardson, Mahmut Uludag, Nathan S Watson-Haigh, Richard Challis, Hiroyuki Nakamura, Emeline Favreau, Esteban A Gómez, Tomáš Pluskal, Guy Leonard, Wolfgang Rumpf, Yannick Wurm.

Sequenceserver: a modern graphical user interface for custom BLAST databases.

Molecular Biology and Evolution 2019;36(12):2922–2924.

doi:10.1093/molbev/msz185 PMID 31411700