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biological-databases [2019/03/12 13:14]
jean-baka
biological-databases [2019/07/01 12:20] (current)
aorth
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-====== Biological ​sequence databases ​on the HPC ======+====== Biological ​Sequence Databases ​on the HPC ======
  
-Some of the most common biological sequence databases are available on the HPCfor you to use with tools like BLAST, etc. Below you can find the list of them, their source URL and the last time they were updated, with links to the update scripts that our system administrator use to perform updates.+~~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.
  
 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        ^Comments ​  ​^Updated¹ ​             ^Database Location ​         ^
 +| nr/nt | NCBI nucleotide collection | 2019-06-20 | ''/​export/​data/​bio/​ncbi/​blast/​db''​ |
 +| nr/nt | NCBI protein collection | 2019-06-20 | ''/​export/​data/​bio/​ncbi/​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 UniRef100 | | ? | ''/​export/​data/​bio/​uniprot/​blast/​db''​ |
 +
 +==== 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 program. For example, to use ''​nt''​ with NCBI ''​blastn'':​
 +
 +<​code>​
 +$ export BLASTDB=/​export/​data/​bio/​ncbi/​blast/​db
 +$ blastn -db nt -query file.seq -out blast.out
 +</​code>​
  
-^Name        ^Version number ​  ^Last updated ​               ^Where it resides ​             ^How to use   ^ +==== Notes ==== 
-|NCBI nr/nt nucleotide collection|N/​A|24 Nov 2018|''/​export/​data/​bio/​ncbi/​blast/​db''​|use ''​BLASTDB=/​export/​data/​bio/​ncbi/​blast/​db''​ in your Bash script| +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''​
-|NCBI nr/nt protein collection|N/​A|16 Aug 2018|''/​export/​data/​bio/​ncbi/blast/db''​|use ''​BLASTDB=/​export/​data/​bio/​ncbi/​blast/​db''​ and ''​blastn ​... -db nt''​ in your Bash script| +
-|UniProt'​s UniProtKB/Swiss-Prot (manually curated, most reliable)|N/A|?​|''/​export/​data/​bio/​uniprot/​blast/​db''​|use ''​BLASTDB=/​export/​data/​bio/​uniprot/​blast/​db''​ and ''​blastp ... -db nr''​ in your Bash script| +
-|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 UniRef100|N/​A|?​|''/​export/​data/​bio/​uniprot/​blast/​db''​|use ''​BLASTDB=/​export/​data/​bio/​uniprot/​blast/​db''​ in your Bash script|+
biological-databases.1552385675.txt.gz · Last modified: 2019/03/12 13:14 by jean-baka