biological-databases
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| biological-databases [2020/04/08 09:39] – aorth | biological-databases [2023/10/09 11:18] (current) – 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. 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. | ||
| - | We endeavor to keep this list updated as the One True List™. | ||
| ^Name ^Comments | ^Name ^Comments | ||
| - | | nt | NCBI nucleotide collection (v5²) | Mar 24, 2020 | ''/ | + | | nt | NCBI nucleotide collection (v5²) | Sep 30, 2023 | ''/ |
| - | | nr | NCBI protein collection (v5²) | Mar 24, 2020 | ''/ | + | | nr | NCBI protein collection (v5²) | Sep 30, 2023 | ''/ |
| - | | UniProt' | + | | UniProt' |
| | UniProt' | | UniProt' | ||
| | UniProt' | | UniProt' | ||
| Line 30: | Line 29: | ||
| 1. Use the following to determine the date of a BLAST database: | 1. Use the following to determine the date of a BLAST database: | ||
| - | < | + | < |
| - | $ blastdbcmd -info -db nt | grep Date | + | $ 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. | + | |
| + | 2. In 2019 [[https:// | ||
| + | ''/ | ||
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