biological-databases
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
biological-databases [2019/03/13 19:49] – aorth | biological-databases [2019/03/13 20:28] – aorth | ||
---|---|---|---|
Line 1: | Line 1: | ||
====== 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. | ||
Line 5: | Line 7: | ||
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 | + | ^Name ^Comments |
- | | NCBI nr/nt nucleotide collection | N/A | 2018-11-24 | ''/ | + | | NCBI nr/nt nucleotide collection | | 2018-11-24 | ''/ |
- | | NCBI nr/nt protein collection | N/A | 2018-08-16 | ''/ | + | | NCBI nr/nt protein collection | | 2018-08-16 | ''/ |
- | | UniProt' | + | | UniProt' |
- | | UniProt' | + | | UniProt' |
- | | UniProt' | + | | UniProt' |
+ | |||
+ | ==== 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 '' | ||
- | ==== Footnotes ==== | + | < |
+ | $ export BLASTDB=/ | ||
+ | $ blastn -db nt -query file.seq -out blast.out | ||
+ | </ | ||
+ | ==== Notes ==== | ||
¹ Use the following to determine the date of a BLAST database: ''/ | ¹ Use the following to determine the date of a BLAST database: ''/ |
biological-databases.txt · Last modified: 2023/10/09 11:18 by aorth