User Tools

Site Tools


biological-databases

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
biological-databases [2019/03/13 23:12]
aorth
biological-databases [2019/07/01 12:20] (current)
aorth
Line 1: Line 1:
 ====== 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.
Line 5: Line 7:
 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 ​+| nr/nt | NCBI nucleotide collection | 2019-06-20 | ''/​export/​data/​bio/​ncbi/​blast/​db''​ | 
-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/nt | NCBI protein collection | 2019-06-20 | ''/​export/​data/​bio/​ncbi/​blast/​db''​ | 
-| 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 | 2019-07-01 ​| ''/​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''​ |
  
 ==== 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 program. For example, to use ''​nt''​ with ''​blastn'':​+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>​ <​code>​
biological-databases.1552507948.txt.gz · Last modified: 2019/03/13 23:12 by aorth