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 revisionPrevious revision
Next revisionBoth sides next revision
biological-databases [2023/10/05 05:42] – aorthbiological-databases [2023/10/05 05:42] – aorth
Line 29: 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:
  
-<code>$ module load blast/2.10.0+ +<code>$ module load blast/2.14.1+ 
-$ 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: 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'' ''/export/data/bio/ncbi/blast/db/v4''
biological-databases.txt · Last modified: 2023/10/09 11:18 by aorth