User Tools

Site Tools


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 09:38]
aorth
biological-databases [2020/04/08 11:14] (current)
aorth
Line 10: Line 10:
 | nt | NCBI nucleotide collection (v5²) | Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5'' | | nt | NCBI nucleotide collection (v5²) | Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5'' |
 | nr | NCBI protein collection (v5²) | Mar 24, 2020 | ''/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+
Line 32: Line 34:
 </code> </code>
  
-  * 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://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.1586338726.txt.gz · Last modified: 2020/04/08 09:38 by aorth