biological-databases
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biological-databases [2019/03/13 19:49] – aorth | biological-databases [2021/12/29 16:14] – 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. | ||
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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 | + | ^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' |
+ | |||
+ | ==== 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 | ||
+ | $ 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 | ||
+ | </ | ||
- | ==== Footnotes ==== | + | 2. In 2019 [[https:// |
- | ¹ Use the following to determine the date of a BLAST database: | + | ''/ |
biological-databases.txt · Last modified: 2023/10/09 11:18 by aorth