BLAST+-Teaching - Revision history

Shtsai at 00:06, 5 April 2026

2026-04-05T00:06:22Z

← Older revision		Revision as of 20:06, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

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

	Teaching		Teaching

	=== Version ===		== Version ==
	<!--		<!--
	2.2.31, 2.10.1, 2.11.0, 2.12.0, 2.13.0, 2.14.0		2.2.31, 2.10.1, 2.11.0, 2.12.0, 2.13.0, 2.14.0
	-->		-->
	2.13.0, 2.14.1, 2.16.0		2.13.0, 2.14.1, 2.16.0
	=== Author / Distributor ===		== Author / Distributor ==

	[http://www.ncbi.nlm.nih.gov/ NCBI]		[http://www.ncbi.nlm.nih.gov/ NCBI]

	=== 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. More information: http://blast.ncbi.nlm.nih.gov/		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 information: http://blast.ncbi.nlm.nih.gov/

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

	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]
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	blastn -num_threads 8 -query example.fasta -out results.out -db nt		blastn -num_threads 8 -query example.fasta -out results.out -db nt
	</pre>		</pre>
	=== Documentation ===		== Documentation ==
	[[#blastn\| jump to blastn]]; [[#blastp\| jump to blastp]]; [[#blastx\| jump to blastx]]; [[#makeblastdb\| jump to makeblastdb]]; [[#top\|Back to Top]]		[[#blastn\| jump to blastn]]; [[#blastp\| jump to blastp]]; [[#blastx\| jump to blastx]]; [[#makeblastdb\| jump to makeblastdb]]; [[#top\|Back to Top]]

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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

Shtsai: /* Documentation */

2026-01-09T19:12:37Z

Documentation

Show changes

Shtsai at 19:10, 9 January 2026

2026-01-09T19:10:48Z

← Older revision		Revision as of 15:10, 9 January 2026
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
	ml BLAST+/2.16.0-gompi-2024a		ml BLAST+/2.16.0-gompi-2024a
	ml ncbiblastdb/~~20250502~~		ml ncbiblastdb/20251103
	blastn [options]		blastn [options]
	</pre>		</pre>
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
	ml BLAST+/2.16.0-gompi-2024a		ml BLAST+/2.16.0-gompi-2024a
	ml ncbiblastdb/~~20250502~~		ml ncbiblastdb/20251103
	blastn -num_threads 8 -query example.fasta -out results.out -db nt		blastn -num_threads 8 -query example.fasta -out results.out -db nt
	</pre>		</pre>

Chelsea at 14:29, 8 July 2025

2025-07-08T14:29:11Z

← Older revision		Revision as of 10:29, 8 July 2025
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	=== Version ===		=== Version ===
			<!--
	2.2.31, 2.10.1, 2.11.0, 2.12.0, 2.13.0, 2.14.0		2.2.31, 2.10.1, 2.11.0, 2.12.0, 2.13.0, 2.14.0
			-->
			2.13.0, 2.14.1, 2.16.0
	=== Author / Distributor ===		=== Author / Distributor ===

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	Datasets are located in the commonly shared "/db" filesystem. NCBI BLAST datasets are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.		Datasets are located in the commonly shared "/db" filesystem. NCBI BLAST datasets are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.

	To use BLAST+ version 2.13.0, please first load the module, for example:		To use BLAST+ version 2.16.0, please first load the module, for example:
	<pre class="gscript">		<pre class="gscript">
	module load BLAST+/2.13.0-gompi-~~2022a~~		module load BLAST+/2.16.0-gompi-2024a
	</pre>		</pre>

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	#SBATCH --error=BLAST+.%j.err		#SBATCH --error=BLAST+.%j.err
	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
	ml BLAST+/2.13.0-gompi-~~2020b~~		ml BLAST+/2.16.0-gompi-2024a
	ml ncbiblastdb/~~20230802~~		ml ncbiblastdb/20250502
	blastn [options]		blastn [options]
	</pre>		</pre>
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	To request cores, use the slurm header #SBATCH --cpus-per-task.		To request cores, use the slurm header #SBATCH --cpus-per-task.

	Below is an example, with -num_threads 8		Below is an example, with -num_threads 8<pre class="gscript">
	<pre class="gscript">
	#!/bin/bash		#!/bin/bash
	#SBATCH --job-name=j_BLAST+_multithread		#SBATCH --job-name=j_BLAST+_multithread
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	#SBATCH --error=BLAST+.%j.err		#SBATCH --error=BLAST+.%j.err
	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
	ml BLAST+/2.13.0-gompi-~~2022a~~		ml BLAST+/2.16.0-gompi-2024a
	ml ncbiblastdb/~~20230802~~		ml ncbiblastdb/20250502
	blastn -num_threads 8 -query example.fasta -out results.out -db nt		blastn -num_threads 8 -query example.fasta -out results.out -db nt
	</pre>		</pre>
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	<span id="blastn"></span>		<span id="blastn"></span>
	<pre class="gcommand">		<pre class="gcommand">
	module load BLAST+/2.13.0-gompi-~~2022a~~		module load BLAST+/2.16.0-gompi-2024a
	blastn -help		blastn -help
	USAGE		USAGE

Chelsea: /* Version */

2024-05-09T14:09:59Z

Version

← Older revision		Revision as of 10:09, 9 May 2024
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	=== Version ===		=== Version ===

	2.12.0, 2.13.0		2.2.31, 2.10.1, 2.11.0, 2.12.0, 2.13.0, 2.14.0

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

Shtsai at 15:53, 5 September 2023

2023-09-05T15:53:12Z

← Older revision		Revision as of 11:53, 5 September 2023
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	=== Running Program ===		=== Running Program ===

	Also refer to [[Running Jobs on ~~Teaching~~]]		Also refer to [[Running Jobs on the teaching cluster]]

	To find all versions of BLAST+ installed on the teaching cluster, please use module spider command to do a search, as shown below:		To find all versions of BLAST+ installed on the teaching cluster, please use module spider command to do a search, as shown below:

Shtsai at 15:52, 5 September 2023

2023-09-05T15:52:26Z

Show changes

Shtsai at 17:20, 27 August 2020

2020-08-27T17:20:48Z

← Older revision		Revision as of 13:20, 27 August 2020
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	=== Version ===		=== Version ===
	2.6.0		2.9.0

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at ~~/usr/local~~/apps/eb/BLAST+/2.6.0-~~foss-2016b~~-~~Python-2.7.14~~		The last version of this application is at /apps/eb/BLAST+/2.9.0-gompi-2019b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml BLAST+/2.6.0-~~foss~~-~~2016b-Python-2.7.14~~		ml BLAST+/2.9.0-gompi-2019b
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml BLAST+/2.6.0-~~foss~~-~~2016b-Python-2.7.14~~<br>		ml BLAST+/2.9.0-gompi-2019b<br>
	blastn <u>[options]</u><br>		blastn <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml BLAST+/2.6.0-~~foss~~-~~2016b-Python-2.7.14~~		ml BLAST+/2.9.0-gompi-2019b
	blastn -h		blastn -h

	USAGE		USAGE
	blastn [-h] [-help] [-import_search_strategy filename]		blastn [-h] [-help] [-import_search_strategy filename]
	[-export_search_strategy filename] [-task task_name] [-db database_name]		[-export_search_strategy filename] [-task task_name] [-db database_name]
	[-dbsize num_letters] [-gilist filename] [-seqidlist filename]		[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
	[-negative_gilist filename] [-entrez_query entrez_query]		[-negative_gilist filename] [-negative_seqidlist filename]
			[-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
			[-negative_taxidlist filename] [-entrez_query entrez_query]
	[-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]		[-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
	[-subject subject_input_file] [-subject_loc range] [-query input_file]		[-subject subject_input_file] [-subject_loc range] [-query input_file]
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	[-perc_identity float_value] [-qcov_hsp_perc float_value]		[-perc_identity float_value] [-qcov_hsp_perc float_value]
	[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]		[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
	[-xdrop_gap_final float_value] [-searchsp int_value]		[-xdrop_gap_final float_value] [-searchsp int_value] [-penalty penalty]
	~~[-sum_stats bool_value~~] [-penalty penalty] [-reward reward] [-no_greedy]		[-reward reward] [-no_greedy] [-min_raw_gapped_score int_value]
	[-min_raw_gapped_score int_value] [-template_type type]		[-template_type type] [-template_length int_value] [-dust DUST_options]
	[-template_length int_value] [-dust DUST_options]
	[-filtering_db filtering_database]		[-filtering_db filtering_database]
	[-window_masker_taxid window_masker_taxid]		[-window_masker_taxid window_masker_taxid]
	[-window_masker_db window_masker_db] [-soft_masking soft_masking]		[-window_masker_db window_masker_db] [-soft_masking soft_masking]
	[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]		[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
	[-best_hit_score_edge float_value] [-window_size int_value]		[-best_hit_score_edge float_value] [-subject_besthit]
	[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]		[-window_size int_value] [-off_diagonal_range int_value]
	[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]		[-use_index boolean] [-index_name string] [-lcase_masking]
	[-outfmt format] [-show_gis] [-num_descriptions int_value]		[-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format]
	[-num_alignments int_value] [-line_length line_length] [-html]		[-show_gis] [-num_descriptions int_value] [-num_alignments int_value]
	[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]		[-line_length line_length] [-html] [-sorthits sort_hits]
	[-version]		[-sorthsps sort_hsps] [-max_target_seqs num_sequences]
			[-num_threads int_value] [-remote] [-version]

	DESCRIPTION		DESCRIPTION
	Nucleotide-Nucleotide BLAST 2.6.0+		Nucleotide-Nucleotide BLAST 2.9.0+

	Use '-help' to print detailed descriptions of command line arguments		Use '-help' to print detailed descriptions of command line arguments

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

Yhuang at 18:02, 10 August 2018

2018-08-10T18:02:03Z

← Older revision		Revision as of 14:02, 10 August 2018
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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+/2.6.0-foss-2016b-Python-2.7.14		ml BLAST+/2.6.0-foss-2016b-Python-2.7.14
	~~blastn~~ blastn -h		blastn -h
	USAGE		USAGE
	blastn [-h] [-help] [-import_search_strategy filename]		blastn [-h] [-help] [-import_search_strategy filename]

Yhuang at 17:41, 10 August 2018

2018-08-10T17:41:08Z

← Older revision		Revision as of 13:41, 10 August 2018
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	The last version of this application is at /usr/local/apps/eb/BLAST+/2.6.0-foss-2016b-Python-2.7.14		The last version of this application is at /usr/local/apps/eb/BLAST+/2.6.0-foss-2016b-Python-2.7.14

	To use this version, please ~~loads~~ the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml BLAST+/2.6.0-foss-2016b-Python-2.7.14		ml BLAST+/2.6.0-foss-2016b-Python-2.7.14
	</pre>		</pre>

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

	<div class="gscript2">		<div class="gscript2">
	<nowiki>#</nowiki>!/bin/bash<br>		<nowiki>#</nowiki>!/bin/bash<br>
	<nowiki>#</nowiki>SBATCH --job-name=~~BLAST~~+<br>		<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+<br>
	<nowiki>#</nowiki>SBATCH --partition=batch<br>		<nowiki>#</nowiki>SBATCH --partition=batch<br>
	<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>		<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>