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biological-databases [2019/07/01 08:06]
aorth
biological-databases [2020/04/08 09:30]
aorth
Line 8: Line 8:
  
 ^Name        ^Comments   ^Updated¹              ^Database Location          ^ ^Name        ^Comments   ^Updated¹              ^Database Location          ^
-| nr/nt | NCBI nucleotide collection | 2019-06-20 | ''/export/data/bio/ncbi/blast/db''+| nr/nt | NCBI nucleotide collection | 2019-06-20 | ''/export/data/bio/ncbi/blast/db/v5''
-| nr/nt | NCBI protein collection | 2019-06-20 | ''/export/data/bio/ncbi/blast/db''+| nr/nt | NCBI protein collection | 2019-06-20 | ''/export/data/bio/ncbi/blast/db/v5''
-| UniProt's UniProtKB/Swiss-Prot | Manually curated, most reliable | | ''/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'' |
 | 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''+---- 
 +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>
biological-databases.txt · Last modified: 2020/04/08 11:14 by aorth