biological-databases
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biological-databases [2019/03/12 10:14] – jean-baka | biological-databases [2019/07/01 09:20] – aorth | ||
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- | ====== Biological | + | ====== Biological |
- | Some of the most common biological sequence databases are available on the HPC, for you to use with tools like BLAST, etc. Below you can find the list of them, their source URL and the last time they were updated, with links to the update scripts that our system administrator use to perform updates. | + | ~~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, | ||
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 ^Comments | ||
+ | | nr/nt | NCBI nucleotide collection | 2019-06-20 | ''/ | ||
+ | | nr/nt | NCBI protein collection | 2019-06-20 | ''/ | ||
+ | | 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 '' | ||
+ | |||
+ | < | ||
+ | $ export BLASTDB=/ | ||
+ | $ blastn -db nt -query file.seq -out blast.out | ||
+ | </ | ||
- | ^Name ^Version number | + | ==== Notes ==== |
- | |NCBI nr/nt nucleotide collection|N/ | + | ¹ Use the following to determine the date of a BLAST database: |
- | |NCBI nr/nt protein collection|N/ | + | |
- | |UniProt' | + | |
- | |UniProt's UniProtKB/ | + | |
- | |UniProt' | + |
biological-databases.txt · Last modified: 2023/10/09 11:18 by aorth