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biological-databases [2019/03/13 23:15]
aorth
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 ======
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 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        ^Comments ​  ^Last Updated¹ ​             ^Database Location ​         ^ +^Name        ^Comments ​  ​^Updated¹ ​             ^Database Location ​         ^ 
-NCBI nr/nt nucleotide collection | | 2018-11-24 | ''/​export/​data/​bio/​ncbi/​blast/​db''​ | +| nr/nt | NCBI nucleotide collection | 2019-06-20 | ''/​export/​data/​bio/​ncbi/​blast/​db''​ | 
-NCBI nr/nt protein collection | | 2018-08-16 | ''/​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 | | ''/​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 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'':​
  
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biological-databases.1552508140.txt.gz · Last modified: 2019/03/13 23:15 by aorth