biological-databases
Differences
This shows you the differences between two versions of the page.
Next revision | Previous revision | ||
biological-databases [2019/03/12 09:22] – created jean-baka | biological-databases [2023/10/09 11:18] (current) – aorth | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | Some of the most common biological sequence databases are available | + | ====== Biological Sequence Databases |
+ | ~~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. | ||
+ | |||
+ | |||
+ | ^Name ^Comments | ||
+ | | nt | NCBI nucleotide collection (v5²) | Sep 30, 2023 | ''/ | ||
+ | | nr | NCBI protein collection (v5²) | Sep 30, 2023 | ''/ | ||
+ | | UniProt' | ||
+ | | UniProt' | ||
+ | | UniProt' | ||
+ | |||
+ | ==== 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=$BLASTDB:/ | ||
+ | $ blastn -db nt -query file.seq -out blast.out | ||
+ | </ | ||
+ | |||
+ | |||
+ | ---- | ||
+ | |||
+ | ==== 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.txt · Last modified: 2023/10/09 11:18 by aorth