BLAST Databases-Sapelo2 - Revision history

Jordan: Removed references to no-longer-available database versions with the "_v5" version suffix as this went away in early 2020.

2026-05-11T19:07:29Z

Removed references to no-longer-available database versions with the "_v5" version suffix as this went away in early 2020.

← Older revision		Revision as of 15:07, 11 May 2026
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	'''Blast database - old version 5'''		'''Blast database - old version 5'''

	~~According to https://ncbiinsights.ncbi.nlm.nih.gov/tag/blastdbv5/, around~~ Feb. 04, 2020 NCBI dropped the _v5 suffix for the v5 Blast databases.		On Feb. 04, 2020 NCBI dropped the _v5 suffix for the v5 Blast databases.

	An old version of the v5 database (download in June 2019) is located at a directory with name pattern as /db/ncbiblast.v5/''dbname'', where ''dbname'' is the name of the database, such as nr, nt, taxdb, refseq_rna, swissprot, etc.

	~~These old versions of the nr and nt databases still have the _v5 suffix, i.e. they are called nr_v5 and nt_v5, respectively.~~

	[[#top\|Back to Top]]		[[#top\|Back to Top]]

Jordan: Updated the list to reflect how the "human_genome" and "mouse_genome" databases have to be referenced since the NCBI couldn't just leave well enough alone.

2025-05-02T13:16:46Z

Updated the list to reflect how the "human_genome" and "mouse_genome" databases have to be referenced since the NCBI couldn't just leave well enough alone.

← Older revision		Revision as of 09:16, 2 May 2025
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	refseq_rna		refseq_rna
	refseq_protein		refseq_protein
	mouse_genome		mouse_genome (which is referenced as "GCF_000001635.27_top_level" when used with BLAST+)
	human_genome		human_genome (which is referenced as "GCF_000001405.39_top_level" when used with BLAST+)
	swissprot		swissprot
	cdd_delta		cdd_delta

Jordan: Updated to reflect the new version of the databases created on 11/01/2024

2024-11-01T18:43:02Z

Updated to reflect the new version of the databases created on 11/01/2024

← Older revision		Revision as of 14:43, 1 November 2024
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	<code>ml spider ncbiblastdb</code>		<code>ml spider ncbiblastdb</code>

	You can then load a database by running the command module load. For example to load the databases timestamped on 08/02/2024:		You can then load a database by running the command module load. For example to load the databases timestamped on 11/02/2024:

	<code>module load ncbiblastdb/~~20240802~~</code>		<code>module load ncbiblastdb/20241102</code>

	Loading this module sets the environment variable BLASTDB to /db/ncbiblast/~~20240802~~. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:		Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20241102. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:
	<div class="gscript2">		<div class="gscript2">
	<nowiki>#</nowiki>!/bin/bash<br>		<nowiki>#</nowiki>!/bin/bash<br>
Line 62:		Line 62:
	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	module load BLAST+/2.14.1-gompi-2023a<br>		module load BLAST+/2.14.1-gompi-2023a<br>
	module load ncbiblastdb/~~20240802~~<br>		module load ncbiblastdb/20241102<br>
	blastn -query example.fasta -out results.out -db nt<br>		blastn -query example.fasta -out results.out -db nt<br>
	</div>		</div>

Jordan at 20:19, 2 August 2024

2024-08-02T20:19:19Z

← Older revision		Revision as of 16:19, 2 August 2024
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	<code>ml spider ncbiblastdb</code>		<code>ml spider ncbiblastdb</code>

	You can then load a database by running the command module load. For example to load the databases timestamped ~~at 06~~/16/~~2021~~:		You can then load a database by running the command module load. For example to load the databases timestamped on 08/02/2024:

	<code>module load ncbiblastdb/~~20210616~~</code>		<code>module load ncbiblastdb/20240802</code>

	Loading this module sets the environment variable BLASTDB to /db/ncbiblast/~~20210616~~. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:		Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20240802. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:
	<div class="gscript2">		<div class="gscript2">
	<nowiki>#</nowiki>!/bin/bash<br>		<nowiki>#</nowiki>!/bin/bash<br>
Line 61:		Line 61:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	module load BLAST+/2.9.0-gompi-~~2019b~~<br>		module load BLAST+/2.14.1-gompi-2023a<br>
	module load ncbiblastdb/~~20220201~~<br>		module load ncbiblastdb/20240802<br>
	blastn -query example.fasta -out results.out -db nt<br>		blastn -query example.fasta -out results.out -db nt<br>
	</div>		</div>
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	In your actual submission script, use your own discretion for the Slurm header values.		In your actual submission script, use your own discretion for the Slurm header values.

	NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets '''every 3 months''' ~~as well as~~ other potentially helpful NCBI BLAST datasets.		NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets '''every 3 months''' along with other potentially helpful NCBI BLAST datasets.

Jordan: Updated the list of available datasets that came with the download on 08/02/2024

2024-08-02T20:15:33Z

Updated the list of available datasets that came with the download on 08/02/2024

@@ Line 3: / Line 3: @@
 '''Blast databases'''
-Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with the name pattern  /db/ncbiblast/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.
+Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with the name pattern  /db/ncbiblast/YYYYMMDD. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. Starting with the download on August 2nd, 2024 (i.e., /db/ncbiblast/20240802), the following databases are currently available and stored together with databases downloaded at the same time:
@@ Line 36: / Line 68: @@
 In your actual submission script, use your own discretion for the Slurm header values.
-NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets '''every 3 months''' as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.
+NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets '''every 3 months''' as well as other potentially helpful NCBI BLAST datasets.

Karen: fixed typo in db path

2022-10-20T20:28:03Z

fixed typo in db path

← Older revision		Revision as of 16:28, 20 October 2022
Line 3:		Line 3:
	'''Blast databases'''		'''Blast databases'''

	Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with the name pattern /db/~~ncbiblasty~~/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.		Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with the name pattern /db/ncbiblast/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.

Moses at 17:55, 6 October 2022

2022-10-06T17:55:29Z

← Older revision		Revision as of 13:55, 6 October 2022
Line 36:		Line 36:
	In your actual submission script, use your own discretion for the Slurm header values.		In your actual submission script, use your own discretion for the Slurm header values.

	NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every ~~month~~ as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.		NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets '''every 3 months''' as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

Keeko: edits for clarity and typo in date

2022-02-17T14:01:15Z

edits for clarity and typo in date

← Older revision		Revision as of 10:01, 17 February 2022
Line 3:		Line 3:
	'''Blast databases'''		'''Blast databases'''

	Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with name pattern as /db/ncbiblasty/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.		Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with the name pattern /db/ncbiblasty/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.


	NCBI BLAST Datasets can be loaded ~~in a similar way to~~ software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:
			NCBI BLAST Datasets can be loaded just like software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:

	<code>ml spider ncbiblastdb</code>		<code>ml spider ncbiblastdb</code>
Line 29:		Line 30:
	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	module load BLAST+/2.9.0-gompi-2019b<br>		module load BLAST+/2.9.0-gompi-2019b<br>
	module load ncbiblastdb/~~20210616~~<br>		module load ncbiblastdb/20220201<br>
	blastn -query example.fasta -out results.out -db nt<br>		blastn -query example.fasta -out results.out -db nt<br>
	</div>		</div>

Keeko at 05:18, 17 February 2022

2022-02-17T05:18:38Z

← Older revision		Revision as of 01:18, 17 February 2022
Line 15:		Line 15:

	Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:		Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:
			<div class="gscript2">
			<nowiki>#</nowiki>!/bin/bash<br>
			<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+<br>
			<nowiki>#</nowiki>SBATCH --partition=batch<br>
			<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>
			<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br>
			<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br>
			<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br>
			<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>
			<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out<br>
			<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err<br>

			cd $SLURM_SUBMIT_DIR<br>
			module load BLAST+/2.9.0-gompi-2019b<br>
			module load ncbiblastdb/20210616<br>
			blastn -query example.fasta -out results.out -db nt<br>
			</div>

			In your actual submission script, use your own discretion for the Slurm header values.

	NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.		NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

Keeko: removed reference to redundant /db/ncbiblast databases organized by name. Added more info about loading databases with modules

2022-02-17T05:17:30Z

removed reference to redundant /db/ncbiblast databases organized by name. Added more info about loading databases with modules

← Older revision		Revision as of 01:17, 17 February 2022
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

	'''Blast ~~database~~'''		'''Blast databases'''

	Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with name pattern as /db/~~ncbiblast~~/~~''dbname''/''~~month-~~day-year''~~, ~~where ''dbname'' is~~ the ~~name of the database, such as~~ nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome, swissprot~~, etc~~. The database refseq_genomic is no longer available to download as a pre-formatted database.		Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with name pattern as /db/ncbiblasty/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.

	~~For example, an nr database downloaded on June 04, 2020 will be available in /db/ncbiblast/nr/06042020.~~

	~~Available databases~~:		NCBI BLAST Datasets can be loaded in a similar way to software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:
	<~~pre class="gscript"~~>
	/db/~~ncbiblast~~/~~human_genome~~/~~03012021~~		<code>ml spider ncbiblastdb</code>
	~~/db/ncbiblast/mouse_genome/03012021~~
	/db/ncbiblast/nr~~/03012021~~		You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:
	~~/db/ncbiblast/nt/03012021~~
	~~/db/ncbiblast/refseq_rna/03012021~~		<code>module load ncbiblastdb/20210616</code>
	~~/db/ncbiblast/~~refseq_protein~~/03012021~~
	~~/db/ncbiblast/~~swissprot~~/03012021~~		Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:
	~~/db/ncbiblast/~~taxdb~~/03012021~~
	~~</pre>~~
			NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.