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biological-databases [2019/07/01 12:20]
aorth
biological-databases [2020/04/08 14:14] (current)
aorth
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 ^Name        ^Comments ​  ​^Updated¹ ​             ^Database Location ​         ^ ^Name        ^Comments ​  ​^Updated¹ ​             ^Database Location ​         ^
-nr/nt | NCBI nucleotide collection | 2019-06-20 ​| ''/​export/​data/​bio/​ncbi/​blast/​db''​ | +| nt | NCBI nucleotide collection ​(v5²) ​Mar 24, 2020 | ''/​export/​data/​bio/​ncbi/​blast/​db/v5''​ | 
-| nr/nt | NCBI protein collection | 2019-06-20 ​| ''/​export/​data/​bio/​ncbi/​blast/​db''​ | +| 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''​ |
  
 ==== Using These Databases ==== ==== Using These Databases ====
-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 NCBI ''​blastn'':​+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>​
  
-==== Notes ==== + 
-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.1561972826.txt.gz · Last modified: 2019/07/01 12:20 by aorth