Shtsai at 00:11, 5 April 2026

2026-04-05T00:11:21Z

← Older revision		Revision as of 20:11, 4 April 2026
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	[[Category:~~Teaching~~]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==
	2.2.26		2.2.26

	=== Author / Distributor ===		== Author / Distributor ==

	[http://blast.ncbi.nlm.nih.gov/ BLAST]		[http://blast.ncbi.nlm.nih.gov/ BLAST]

	=== Description ===		== 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."		"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 [http://blast.ncbi.nlm.nih.gov/ BLAST]		More details are at [http://blast.ncbi.nlm.nih.gov/ BLAST]

	=== Running Program ===		== Running Program ==

	The last version of this application is at /apps/eb/BLAST/2.2.26-Linux_x86_64		The last version of this application is at /apps/eb/BLAST/2.2.26-Linux_x86_64
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Source code is obtained from [http://blast.ncbi.nlm.nih.gov/ BLAST]		Source code is obtained from [http://blast.ncbi.nlm.nih.gov/ BLAST]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Chelsea: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.2.26 === Author / Distributor === [http://blast.ncbi.nlm.nih.gov/ BLAST] === 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..."

2024-05-14T15:32:46Z

Created page with "Category:Teaching Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.2.26 === Author / Distributor === [http://blast.ncbi.nlm.nih.gov/ BLAST] === 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..."

New page

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
2.2.26

=== Author / Distributor ===

[http://blast.ncbi.nlm.nih.gov/ BLAST]

=== 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 [http://blast.ncbi.nlm.nih.gov/ BLAST]

=== Running Program ===

The last version of this application is at /apps/eb/BLAST/2.2.26-Linux_x86_64

To use this version, please load the module with
<pre class="gscript">
ml BLAST/2.2.26-Linux_x86_64
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST.%j.err 

cd $SLURM_SUBMIT_DIR 
ml BLAST/2.2.26-Linux_x86_64 
blastall [options] 
</div>
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]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
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

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://blast.ncbi.nlm.nih.gov/ BLAST]

=== System ===
64-bit Linux

BLAST-Sapelo2 - Revision history

Shtsai at 00:11, 5 April 2026