biological-databases
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biological-databases [2019/03/13 20:11] – aorth | biological-databases [2023/10/09 11:18] (current) – aorth | ||
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====== Biological Sequence Databases on the HPC ====== | ====== Biological Sequence Databases on the HPC ====== | ||
+ | |||
+ | ~~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. | ||
- | We endeavor to keep this list updated as the One True List™. | ||
- | ^Name ^Version Number | + | ^Name ^Comments |
- | | NCBI nr/nt nucleotide collection | N/A | 2018-11-24 | + | | nt | NCBI nucleotide collection |
- | | NCBI nr/nt protein collection | N/A | 2018-08-16 | + | | nr | NCBI protein collection |
- | | UniProt' | + | | UniProt' |
- | | UniProt' | + | | UniProt' |
- | | UniProt' | + | | UniProt' |
- | To use these databases you generally need to set an environment variable | + | ==== Using These Databases ==== |
+ | Tools like BLAST use the '' | ||
+ | |||
+ | If you are using different software you will need to set the variable manually, for example: | ||
< | < | ||
- | $ export BLASTDB=/ | + | $ export BLASTDB=$BLASTDB:/ |
$ blastn -db nt -query file.seq -out blast.out | $ blastn -db nt -query file.seq -out blast.out | ||
</ | </ | ||
- | < | ||
- | <hr /> | ||
- | </ | ||
- | ¹ Use the following to determine the date of a BLAST database: | + | ---- |
+ | |||
+ | ==== Notes ===== | ||
+ | 1. Use the following to determine the date of a BLAST database: | ||
+ | |||
+ | < | ||
+ | $ blastdbcmd -info -db nt | grep Date</ | ||
+ | |||
+ | 2. In 2019 [[https:// | ||
+ | |||
+ | ''/ |
biological-databases.1552507900.txt.gz · Last modified: 2019/03/13 20:11 by aorth