Difference between revisions of "BLAST Databases-Sapelo2"
(added more clarity on what a blast db is and that refseq_genomic is unavailable.) |
(removed reference to redundant /db/ncbiblast databases organized by name. Added more info about loading databases with modules) |
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[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]] | [[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]] | ||
| − | '''Blast | + | '''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/ | + | 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. |
| − | |||
| − | + | 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: | |
| − | < | + | |
| − | / | + | <code>ml spider ncbiblastdb</code> |
| − | + | ||
| − | /db/ncbiblast/nr | + | You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021: |
| − | + | ||
| − | + | <code>module load ncbiblastdb/20210616</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: | |
| − | + | ||
| − | + | ||
| + | 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. | ||
Revision as of 01:17, 17 February 2022
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.
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:
ml spider ncbiblastdb
You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:
module load ncbiblastdb/20210616
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:
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.
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.
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.