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biological-databases [2019/03/13 20:28]
aorth
biological-databases [2020/04/08 11:14] (current)
aorth
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 ^Name        ^Comments   ^Updated¹              ^Database Location          ^ ^Name        ^Comments   ^Updated¹              ^Database Location          ^
-| NCBI nr/nt nucleotide collection | | 2018-11-24 | ''/export/data/bio/ncbi/blast/db''+| nt | NCBI nucleotide collection (v5²) Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5''
-NCBI nr/nt protein collection | | 2018-08-16 | ''/export/data/bio/ncbi/blast/db''+| nr | NCBI protein collection (v5²) Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5''
-| UniProt's UniProtKB/Swiss-Prot | Manually curated, most reliable | | ''/export/data/bio/uniprot/blast/db'' |+| UniProt's UniProtKB/Swiss-Prot | Manually curated, most reliable | July 1, 2019 | ''/export/data/bio/uniprot/blast/db'' |
 | UniProt's UniProtKB/TrEMBL | Automated curation | ? | ''/export/data/bio/uniprot/blast/db'' | | UniProt's UniProtKB/TrEMBL | Automated curation | ? | ''/export/data/bio/uniprot/blast/db'' |
 | UniProt's UniRef100 | | ? | ''/export/data/bio/uniprot/blast/db'' | | UniProt's UniRef100 | | ? | ''/export/data/bio/uniprot/blast/db'' |
  
 ==== Using These Databases ==== ==== 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 programFor example, to use ''nt'' with NCBI ''blastn'':+Tools like BLAST use the ''BLASTDB'' environment variable to find the location of the system's BLAST databasesILRI's BLAST environment modules like ''blast/2.10.0+'' automatically set this variable when you load the module. 
 + 
 +If you are using different software you will need to set the variable manually, for example:
  
 <code> <code>
-$ export BLASTDB=/export/data/bio/ncbi/blast/db+$ export BLASTDB=$BLASTDB:/export/data/bio/ncbi/blast/db/v5
 $ blastn -db nt -query file.seq -out blast.out $ blastn -db nt -query file.seq -out blast.out
 </code> </code>
  
-==== Notes ==== + 
-¹ Use the following to determine the date of a BLAST database: ''/export/apps/blast/2.7.1+/bin/blastdbcmd -info -db nt | grep Date''+---- 
 + 
 +==== Notes ===== 
 +1. Use the following to determine the date of a BLAST database: 
 + 
 +<code>$ module load blast/2.10.0+ 
 +blastdbcmd -info -db nt | grep Date 
 +</code> 
 + 
 +2. In 2019 [[https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/24/have-you-tried-blast-2-9-0-and-version-5-blast-databases-dbv5/|NCBI introduced BLAST database format version 5]] and these only work with BLAST tools starting from 2.9.0. NCBI are no longer updating the version 4 databases, but we have preserved them in a separate directory if you are using tools that do not support version 5: 
 + 
 +''/export/data/bio/ncbi/blast/db/v4''
biological-databases.1552508928.txt.gz · Last modified: 2019/03/13 20:28 by aorth