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biological-databases [2020/04/08 09:35]
aorth 		biological-databases [2020/04/08 09:56]
aorth
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 ^Name        ^Comments   ^Updated¹              ^Database Location          ^ ^Name        ^Comments   ^Updated¹              ^Database Location          ^
-| nt | NCBI nucleotide collection (v5) | 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 (v5) | 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 | 2019-07-01 | ''/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'' |
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 </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.txt · Last modified: 2020/04/08 11:14 by aorth

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