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biological-databases [2019/03/13 23:11] aorth |
biological-databases [2019/07/01 11:06] aorth |
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| ====== Biological Sequence Databases on the HPC ====== | ====== Biological Sequence Databases on the HPC ====== | ||
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| + | ~~NOTOC~~ | ||
| Some of the most common biological sequence databases are available on the HPC for you to use with tools like BLAST. Below you can find the list of them, their location on the system, and the last time they were updated. | Some of the most common biological sequence databases are available on the HPC for you to use with tools like BLAST. Below you can find the list of them, their location on the system, and the last time they were updated. | ||
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| We endeavor to keep this list updated as the One True List™. | We endeavor to keep this list updated as the One True List™. | ||
| - | ^Name ^Version Number ^Last Updated¹ ^Database Location ^How to Use ^ | + | ^Name ^Comments ^Updated¹ ^Database Location ^ |
| - | | NCBI nr/nt nucleotide collection | N/A | 2018-11-24 | ''/export/data/bio/ncbi/blast/db'' | Use ''BLASTDB=/export/data/bio/ncbi/blast/db'' and ''blastn ... -db nt'' in your Bash script | | + | | nr/nt | NCBI nucleotide collection | 2019-06-20 | ''/export/data/bio/ncbi/blast/db'' | |
| - | | NCBI nr/nt protein collection | N/A | 2018-08-16 | ''/export/data/bio/ncbi/blast/db'' | use ''BLASTDB=/export/data/bio/ncbi/blast/db'' and ''blastp ... -db nr'' in your Bash script | | + | | nr/nt | NCBI protein collection | 2019-06-20 | ''/export/data/bio/ncbi/blast/db'' | |
| - | | UniProt's UniProtKB/Swiss-Prot (manually curated, most reliable) | N/A | ? | ''/export/data/bio/uniprot/blast/db'' | use ''BLASTDB=/export/data/bio/uniprot/blast/db'' in your Bash script | | + | | UniProt's UniProtKB/Swiss-Prot | Manually curated, most reliable | ? | ''/export/data/bio/uniprot/blast/db'' | |
| - | | UniProt's UniProtKB/TrEMBL (automated curation) | N/A | ? | ''/export/data/bio/uniprot/blast/db'' | use ''BLASTDB=/export/data/bio/uniprot/blast/db'' in your Bash script | | + | | UniProt's UniProtKB/TrEMBL | Automated curation | ? | ''/export/data/bio/uniprot/blast/db'' | |
| - | | UniProt's UniRef100 | N/A | ? | ''/export/data/bio/uniprot/blast/db'' | use ''BLASTDB=/export/data/bio/uniprot/blast/db'' in your Bash script | | + | | UniProt's UniRef100 | | ? | ''/export/data/bio/uniprot/blast/db'' | |
| - | To use these databases you generally need to set an environment variable pointing to the location of the database before running your program. For example, to use ''nt'' with ''blastn'': | + | ==== Using These Databases ==== |
| + | To use these databases you generally need to set an environment variable pointing to the location of the database before running your program. For example, to use ''nt'' with NCBI ''blastn'': | ||
| <code> | <code> | ||
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| </code> | </code> | ||
| - | <html> | + | ==== Notes ==== |
| - | <hr /> | + | |
| - | </html> | + | |
| ¹ Use the following to determine the date of a BLAST database: ''/export/apps/blast/2.7.1+/bin/blastdbcmd -info -db nt | grep Date'' | ¹ Use the following to determine the date of a BLAST database: ''/export/apps/blast/2.7.1+/bin/blastdbcmd -info -db nt | grep Date'' | ||
biological-databases.txt · Last modified: 2020/04/08 14:14 by aorth
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