BLAST

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The blast suite is made up of the following programs:

Contents


bl2seq

bl2seq 2.2.26 arguments:

 -i  First sequence [File In]
 -j  Second sequence [File In]
 -p  Program name: blastp, blastn, blastx, tblastn, tblastx. For blastx 1st sequence should be nucleotide, tblastn 2nd sequence nucleotide [String]
 -g  Gapped [T/F]
   default = T
 -o  alignment output file [File Out]
   default = stdout
 -d  theor. db size (zero is real size) [Real]
   default = 0
 -a  Text ASN.1 output file [File Out]  Optional
 -G  Cost to open a gap (-1 invokes default behavior) [Integer]
   default = -1
 -E  Cost to extend a gap (-1 invokes default behavior) [Integer]
   default = -1
 -X  X dropoff value for gapped alignment (in bits) (zero invokes default behavior)
     blastn 30, megablast 20, tblastx 0, all others 15 [Integer]
   default = 0
 -W  Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer]
   default = 0
 -M  Matrix [String]
   default = BLOSUM62
 -q  Penalty for a nucleotide mismatch (blastn only) [Integer]
   default = -3
 -r  Reward for a nucleotide match (blastn only) [Integer]
   default = 1
 -F  Filter query sequence (DUST with blastn, SEG with others) [String]
   default = T
 -e  Expectation value (E) [Real]
   default = 10.0
 -S  Query strands to search against database (blastn only).  3 is both, 1 is top, 2 is bottom [Integer]
   default = 3
 -T  Produce HTML output [T/F]
   default = F
 -m  Use Mega Blast for search [T/F]  Optional
   default = F
 -Y  Effective length of the search space (use zero for the real size) [Real]
   default = 0
 -t  Length of the largest intron allowed in tblastn for linking HSPs [Integer]
   default = 0
 -I  Location on first sequence [String]  Optional
 -J  Location on second sequence [String]  Optional
 -D  Output format: 0 - traditional, 1 - tabular [Integer]
   default = 0
 -U  Use lower case filtering for the query sequence [T/F]  Optional
   default = F
 -A  Input sequences in the form of accession.version [T/F]
   default = F
 -V  Force use of the legacy BLAST engine [T/F]  Optional
   default = F


blastall

blastall 2.2.26 arguments:

 -p  Program Name [String]
 -d  Database [String]
   default = nr
 -i  Query File [File In]
   default = stdin
 -e  Expectation value (E) [Real]
   default = 10.0
 -m  alignment view options:
  0 = pairwise,
  1 = query-anchored showing identities,
  2 = query-anchored no identities,
  3 = flat query-anchored, show identities,
  4 = flat query-anchored, no identities,
  5 = query-anchored no identities and blunt ends,
  6 = flat query-anchored, no identities and blunt ends,
  7 = XML Blast output,
  8 = tabular,
  9 tabular with comment lines
  10 ASN, text
  11 ASN, binary [Integer]
   default = 0
   range from 0 to 11
 -o  BLAST report Output File [File Out]  Optional
   default = stdout
 -F  Filter query sequence (DUST with blastn, SEG with others) [String]
   default = T
 -G  Cost to open a gap (-1 invokes default behavior) [Integer]
   default = -1
 -E  Cost to extend a gap (-1 invokes default behavior) [Integer]
   default = -1
 -X  X dropoff value for gapped alignment (in bits) (zero invokes default behavior)
     blastn 30, megablast 20, tblastx 0, all others 15 [Integer]
   default = 0
 -I  Show GI's in deflines [T/F]
   default = F
 -q  Penalty for a nucleotide mismatch (blastn only) [Integer]
   default = -3
 -r  Reward for a nucleotide match (blastn only) [Integer]
   default = 1
 -v  Number of database sequences to show one-line descriptions for (V) [Integer]
   default = 500
 -b  Number of database sequence to show alignments for (B) [Integer]
   default = 250
 -f  Threshold for extending hits, default if zero
     blastp 11, blastn 0, blastx 12, tblastn 13
     tblastx 13, megablast 0 [Real]
   default = 0
 -g  Perform gapped alignment (not available with tblastx) [T/F]
   default = T
 -Q  Query Genetic code to use [Integer]
   default = 1
 -D  DB Genetic code (for tblast[nx] only) [Integer]
   default = 1
 -a  Number of processors to use [Integer]
   default = 1
 -O  SeqAlign file [File Out]  Optional
 -J  Believe the query defline [T/F]
   default = F
 -M  Matrix [String]
   default = BLOSUM62
 -W  Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer]
   default = 0
 -z  Effective length of the database (use zero for the real size) [Real]
   default = 0
 -K  Number of best hits from a region to keep. Off by default.

If used a value of 100 is recommended. Very high values of -v or -b is also suggested [Integer]

   default = 0
 -P  0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer]
   default = 0
 -Y  Effective length of the search space (use zero for the real size) [Real]
   default = 0
 -S  Query strands to search against database (for blast[nx], and tblastx)
      3 is both, 1 is top, 2 is bottom [Integer]
   default = 3
 -T  Produce HTML output [T/F]
   default = F
 -l  Restrict search of database to list of GI's [String]  Optional
 -U  Use lower case filtering of FASTA sequence [T/F]  Optional
 -y  X dropoff value for ungapped extensions in bits (0.0 invokes default behavior)
     blastn 20, megablast 10, all others 7 [Real]
   default = 0.0
 -Z  X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)
     blastn/megablast 100, tblastx 0, all others 25 [Integer]
   default = 0
 -R  PSI-TBLASTN checkpoint file [File In]  Optional
 -n  MegaBlast search [T/F]
   default = F
 -L  Location on query sequence [String]  Optional
 -A  Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer]
   default = 0
 -w  Frame shift penalty (OOF algorithm for blastx) [Integer]
   default = 0
 -t  Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments. (0 invokes default behavior; a negative value disables linking.) [Integer]
   default = 0
 -B  Number of concatenated queries, for blastn and tblastn [Integer]  Optional
   default = 0
 -V  Force use of the legacy BLAST engine [T/F]  Optional
   default = F
 -C  Use composition-based score adjustments for blastp or tblastn:
     As first character:
     D or d: default (equivalent to T)
     0 or F or f: no composition-based statistics
     2 or T or t: Composition-based score adjustments as in Bioinformatics 21:902-911,
     1: Composition-based statistics as in NAR 29:2994-3005, 2001
         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.
          As second character, if first character is equivalent to 1, 2, or 3:
     U or u: unified p-value combining alignment p-value and compositional p-value in round 1 only
[String]
   default = D
 -s  Compute locally optimal Smith-Waterman alignments (This option is only
     available for gapped tblastn.) [T/F]
   default = F


fastacmd

formatrpsdb

formatrpsdb 2.2.26 arguments:

 -t  Title for database file [String]  Optional
 -i  Input file containing list of ASN.1 Scoremat filenames [File In]
 -l  Logfile name [File Out]  Optional
   default = formatrpsdb.log
 -o  Create index files for database [T/F]  Optional
   default = F
 -v  Database volume size in millions of letters [Integer]  Optional
   default = 0
   range from 0 to ?
 -b  Scoremat files are binary [T/F]  Optional
   default = F
 -f  Threshold for extending hits for RPS database [Real]  Optional
   default = 11.0
 -n  Base name of output database (same as input file if not specified) [String]  Optional
 -S  For scoremats that contain only residue frequencies, the scaling factor to apply when creating PSSMs [Real]  Optional
   default = 100.0
 -G  The gap opening penalty (if not present in the scoremat) [Integer]  Optional
   default = 11
 -E  The gap extension penalty (if not present in the scoremat) [Integer]  Optional
   default = 1
 -U  Underlying score matrix (if not present in the scoremat) [String]  Optional
   default = BLOSUM62


megablast

megablast 2.2.26 arguments:

 -d  Database [String]
   default = nr
 -i  Query File [File In]
 -e  Expectation value [Real]
   default = 10.0
 -m  alignment view options:
  0 = pairwise,
  1 = query-anchored showing identities,
  2 = query-anchored no identities,
  3 = flat query-anchored, show identities,
  4 = flat query-anchored, no identities,
  5 = query-anchored no identities and blunt ends,
  6 = flat query-anchored, no identities and blunt ends,
  7 = XML Blast output,
  8 = tabular,
  9 tabular with comment lines,
  10 ASN, text
  11 ASN, binary [Integer]
   default = 0
   range from 0 to 11
 -o  BLAST report Output File [File Out]  Optional
   default = stdout
 -F  Filter query sequence [String]
   default = T
 -X  X dropoff value for gapped alignment (in bits) [Integer]
   default = 20
 -I  Show GI's in deflines [T/F]
   default = F
 -q  Penalty for a nucleotide mismatch [Integer]
   default = -3
 -r  Reward for a nucleotide match [Integer]
   default = 1
 -v  Number of database sequences to show one-line descriptions for (V) [Integer]
   default = 500
 -b  Number of database sequence to show alignments for (B) [Integer]
   default = 250
 -D  Type of output:
  0 - alignment endpoints and score,
  1 - all ungapped segments endpoints,
  2 - traditional BLAST output,
  3 - tab-delimited one line format,
  4 - incremental text ASN.1,
  5 - incremental binary ASN.1 [Integer]
   default = 2
 -a  Number of processors to use [Integer]
   default = 1
 -O  ASN.1 SeqAlign file; must be used in conjunction with -D2 option [File Out]  Optional
 -J  Believe the query defline [T/F]  Optional
   default = F
 -M  Maximal total length of queries for a single search [Integer]
   default = 5000000
 -W  Word size (length of best perfect match) [Integer]
   default = 28
 -z  Effective length of the database (use zero for the real size) [Real]
   default = 0
 -Y  Effective length of the search space (use zero for the real size) [Real]
   default = 0
 -P  Maximal number of positions for a hash value (set to 0 to ignore) [Integer]
   default = 0
 -S  Query strands to search against database: 3 is both, 1 is top, 2 is bottom [Integer]
   default = 3
 -T  Produce HTML output [T/F]
   default = F
 -l  Restrict search of database to list of GI's [String]  Optional
 -G  Cost to open a gap (-1 invokes default behavior) [Integer]
   default = -1
 -E  Cost to extend a gap (-1 invokes default behavior) [Integer]
   default = -1
 -s  Minimal hit score to report (0 for default behavior) [Integer]
   default = 0
 -Q  Masked query output, must be used in conjunction with -D 2 option [File Out]  Optional
 -f  Show full IDs in the output (default - only GIs or accessions) [T/F]
   default = F
 -U  Use lower case filtering of FASTA sequence [T/F]  Optional
   default = F
 -R  Report the log information at the end of output [T/F]  Optional
   default = F
 -p  Identity percentage cut-off [Real]
   default = 0
 -L  Location on query sequence [String]  Optional
 -A  Multiple Hits window size; default is 0 (i.e. single-hit extensions) or 40 for discontiguous template (negative number overrides this) [Integer]
   default = 0
 -y  X dropoff value for ungapped extension [Integer]
   default = 10
 -Z  X dropoff value for dynamic programming gapped extension [Integer]
   default = 50
 -t  Length of a discontiguous word template (contiguous word if 0) [Integer]
   default = 0
 -g  Make discontiguous megablast generate words for every base of the database (mandatory with the current BLAST engine) [T/F]  Optional
   default = T
 -n  Use non-greedy (dynamic programming) extension for affine gap scores [T/F]  Optional
   default = F
 -N  Type of a discontiguous word template (0 - coding, 1 - optimal, 2 - two simultaneous [Integer]
   default = 0
 -H  Maximal number of HSPs to save per database sequence (0 = unlimited) [Integer]
   default = 0
 -V  Force use of the legacy BLAST engine [T/F]  Optional
   default = F


rpsblast

rpsblast 2.2.26 arguments:

 -i  Input query sequence (this parameter must be set) [File In]
   default = stdin
 -d  RPS BLAST Database [File In]
 -p  Query sequence is protein  [T/F]  Optional
   default = T
 -e  Expectation value (E) [Real]
   default = 10.0
 -m  alignment view options:
  0 = pairwise,
  1 = query-anchored showing identities,
  2 = query-anchored no identities,
  3 = flat query-anchored, show identities,
  4 = flat query-anchored, no identities,
  5 = query-anchored no identities and blunt ends,
  6 = flat query-anchored, no identities and blunt ends,
  7 = XML Blast output,
  8 = tabular output,
  9 = tabular output with comments [Integer]
   default = 0
 -o  Output File for Alignment [File Out]  Optional
   default = stdout
 -y  Dropoff (X) for blast extensions in bits (default if zero) [Real]
   default = 7.0
 -P  0 for multiple hit, 1 for single hit [Integer]
   default = 0
 -F  Filter query sequence with SEG [String]
   default = F
 -X  X dropoff value for gapped alignment (in bits) [Integer]
   default = 15
 -N  Number of bits to trigger gapping [Real]
   default = 22.0
 -a  Number of processors to use [Integer]
   default = 1
 -I  Show GI's in deflines [T/F]
   default = F
 -J  Believe the query defline [T/F]
   default = F
 -Z  X dropoff value for final gapped alignment (in bits) [Integer]
   default = 25
 -O  SeqAlign file ('Believe the query defline' must be TRUE) [File Out]  Optional
 -v  Number of database sequences to show one-line descriptions for (V) [Integer]
   default = 500
 -b  Number of database sequence to show alignments for (B) [Integer]
   default = 250
 -z  Effective length of the database (use zero for the real size) [Real]
   default = 0
 -Y  Effective length of the search space (use zero for the real size) [Real]
   default = 0
 -T  Produce HTML output [T/F]
   default = F
 -l  Logfile name  [File Out]  Optional
   default = stderr
 -U  Use lower case filtering of FASTA sequence [T/F]  Optional
   default = F
 -L  Range restriction on query sequence (Format: start,stop) blastp only
     0 in 'start' refers to the beginning of the sequence
     0 in 'stop' refers to the end of the sequence [String]  Optional
   default = 0,0