ILRI Research Computing

User Tools

Site Tools

You are here: start » biological-databases
biological-databases

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
biological-databases [2020/04/08 09:31]
aorth 		biological-databases [2020/04/08 11:14] (current)
aorth
Line 8: Line 8:
  
 ^Name        ^Comments   ^Updated¹              ^Database Location          ^ ^Name        ^Comments   ^Updated¹              ^Database Location          ^
-| nr/nt | NCBI nucleotide collection | 2019-06-20 | ''/export/data/bio/ncbi/blast/db/v5'' | +| nt | NCBI nucleotide collection (v5²) | Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5'' | 
-| nr/nt | NCBI protein collection | 2019-06-20 | ''/export/data/bio/ncbi/blast/db/v5'' | +| nr | NCBI protein collection (v5²) | Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5'' | 
-| UniProt's UniProtKB/Swiss-Prot | Manually curated, most reliable | 2019-07-01 | ''/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'' |
Line 24: Line 24:
 </code> </code>
  
 +
 +----
  
 ==== Notes ===== ==== Notes =====
-¹ Use the following to determine the date of a BLAST database:+1. Use the following to determine the date of a BLAST database:
  
 <code>$ module load blast/2.10.0+ <code>$ module load blast/2.10.0+
 $ blastdbcmd -info -db nt | grep Date $ blastdbcmd -info -db nt | grep Date
 </code> </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.1586338286.txt.gz · Last modified: 2020/04/08 09:31 by aorth

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International
CC Attribution-Noncommercial-Share Alike 4.0 International Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki