BLAST-Teaching: Difference between revisions
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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=BLAST.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=BLAST.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=BLAST.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml BLAST/2.2.26-Linux_x86_64 | ml BLAST/2.2.26-Linux_x86_64 | ||
blastall --help | |||
blastall 2.2.26 arguments: | blastall 2.2.26 arguments: |
Revision as of 14:01, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.2.26
Author / Distributor
Description
"Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences." More details are at BLAST
Running Program
The last version of this application is at /usr/local/apps/eb/BLAST/2.2.26-Linux_x86_64
To use this version, please load the module with
ml BLAST/2.2.26-Linux_x86_64
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_BLAST
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST.%j.out
#SBATCH --error=BLAST.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST/2.2.26-Linux_x86_64
blastall [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml BLAST/2.2.26-Linux_x86_64 blastall --help 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
Installation
Source code is obtained from BLAST
System
64-bit Linux