biological-databases
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biological-databases [2019/07/01 08:06] – aorth | biological-databases [2020/04/08 09:38] – aorth | ||
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^Name ^Comments | ^Name ^Comments | ||
- | | nr/nt | NCBI nucleotide collection | 2019-06-20 | + | | nt | NCBI nucleotide collection |
- | | nr/nt | NCBI protein collection | 2019-06-20 | + | | nr | NCBI protein collection |
- | | UniProt' | + | | UniProt' |
| UniProt' | | UniProt' | ||
| UniProt' | | UniProt' | ||
==== Using These Databases ==== | ==== Using These Databases ==== | ||
- | To use these databases you generally need to set an environment variable | + | Tools like BLAST use the '' |
+ | |||
+ | If you are using different software you will need to set the variable manually, for example: | ||
< | < | ||
- | $ export BLASTDB=/ | + | $ export BLASTDB=$BLASTDB:/ |
$ blastn -db nt -query file.seq -out blast.out | $ blastn -db nt -query file.seq -out blast.out | ||
</ | </ | ||
- | ==== Notes ==== | + | |
- | ¹ Use the following to determine the date of a BLAST database: | + | ==== 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