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