biological-databases
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biological-databases [2019/03/12 09:22] – created jean-baka | biological-databases [2020/04/08 09:39] – aorth | ||
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- | 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, | + | ====== 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, | ||
+ | |||
+ | We endeavor to keep this list updated as the One True List™. | ||
+ | |||
+ | ^Name ^Comments | ||
+ | | nt | NCBI nucleotide collection (v5²) | Mar 24, 2020 | ''/ | ||
+ | | nr | NCBI protein collection (v5²) | Mar 24, 2020 | ''/ | ||
+ | | 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: NCBI introduced database format version 5 in 2019 and these only work with BLAST tools starting from 2.9.0. They are no longer updating the version 4 databses, but we have preserved them in a separate directory if you are using tools that do not support version 5. | ||
biological-databases.txt · Last modified: 2023/10/09 11:18 by aorth