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biological-databases [2020/04/08 09:35] – aorthbiological-databases [2023/10/09 11:18] (current) – aorth
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 Some of the most common biological sequence databases are available on the HPC for you to use with tools like BLAST. Below you can find the list of them, their location on the system, and the last time they were updated. Some of the most common biological sequence databases are available on the HPC for you to use with tools like BLAST. Below you can find the list of them, their location on the system, and the last time they were updated.
  
-We endeavor to keep this list updated as the One True List™. 
  
 ^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) | Sep 30, 2023 | ''/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) | Sep 30, 2023 | ''/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'' |
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 ==== 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/2.14.1+ 
-$ 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: 
 + 
 +''/export/data/bio/ncbi/blast/db/v4''
biological-databases.1586338549.txt.gz · Last modified: by aorth