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biological-databases [2019/03/13 20:11]
aorth
biological-databases [2020/04/08 11:14]
aorth
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 ====== Biological Sequence Databases on the HPC ====== ====== Biological Sequence Databases on the HPC ======
 +
 +~~NOTOC~~
  
 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.
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 We endeavor to keep this list updated as the One True List™. We endeavor to keep this list updated as the One True List™.
  
-^Name        ^Version Number   ^Last Updated¹              ^Database Location          ^How to Use   +^Name        ^Comments   ^Updated¹              ^Database Location          ^ 
-| NCBI nr/nt nucleotide collection | N/A | 2018-11-24 | ''/export/data/bio/ncbi/blast/db'' | Use ''BLASTDB=/export/data/bio/ncbi/blast/db'' and ''blastn ... -db nt'' in your Bash script +| nt | NCBI nucleotide collection (v5²) Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5''
-| NCBI nr/nt protein collection | N/A | 2018-08-16 | ''/export/data/bio/ncbi/blast/db'' | use ''BLASTDB=/export/data/bio/ncbi/blast/db'' and ''blastp ... -db nr'' in your Bash script +| nr | NCBI protein collection (v5²) Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5''
-| UniProt's UniProtKB/Swiss-Prot (manually curated, most reliableN/A | ? | ''/export/data/bio/uniprot/blast/db'' | use ''BLASTDB=/export/data/bio/uniprot/blast/db'' in your Bash script +| UniProt's UniProtKB/Swiss-Prot | Manually curated, most reliable | July 1, 2019 | ''/export/data/bio/uniprot/blast/db''
-| UniProt's UniProtKB/TrEMBL (automated curation) | N/A | ? | ''/export/data/bio/uniprot/blast/db'' | use ''BLASTDB=/export/data/bio/uniprot/blast/db'' in your Bash script +| UniProt's UniProtKB/TrEMBL | Automated curation | ? | ''/export/data/bio/uniprot/blast/db''
-| UniProt's UniRef100 | N/A | ? | ''/export/data/bio/uniprot/blast/db'' | use ''BLASTDB=/export/data/bio/uniprot/blast/db'' in your Bash script |+| UniProt's UniRef100 | | ? | ''/export/data/bio/uniprot/blast/db'' |
  
-To use these databases you generally need to set an environment variable pointing to the location of the database before running your programFor example, to use ''nt'' with ''blastn'':+==== Using These Databases ==== 
 +Tools like BLAST use the ''BLASTDB'' environment variable to find the location of the system's BLAST databasesILRI's BLAST environment modules like ''blast/2.10.0+'' automatically set this variable when you load the module. 
 + 
 +If you are using different software you will need to set the variable manually, for example:
  
 <code> <code>
-$ export BLASTDB=/export/data/bio/ncbi/blast/db+$ export BLASTDB=$BLASTDB:/export/data/bio/ncbi/blast/db/v5
 $ blastn -db nt -query file.seq -out blast.out $ blastn -db nt -query file.seq -out blast.out
 </code> </code>
  
-<html> 
-<hr /> 
-</html> 
  
-¹ Use the following to determine the date of a BLAST database: ''/export/apps/blast/2.7.1+/bin/blastdbcmd -info -db nt | grep Date''+---- 
 + 
 +==== Notes ===== 
 +1. Use the following to determine the date of a BLAST database: 
 + 
 +<code>$ module load blast/2.10.0+ 
 +blastdbcmd -info -db nt | grep Date 
 +</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