ILRI Research Computing

User Tools

Site Tools

You are here: start » biological-databases
biological-databases

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revisionBoth sides next revision
biological-databases [2019/03/13 19:42] – aorthbiological-databases [2019/03/13 19:45] – aorth
Line 5: Line 5:
 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                ^Where it resides              ^How to use   ^ +^Name        ^Version Number   ^Last Updated¹                ^Where it Resides              ^How to Use   ^ 
-|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| +| 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 | 
-|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| +| 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 | 
-|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'' 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'' 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 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|+| UniProt's UniRef100 | N/A | ? | ''/export/data/bio/uniprot/blast/db'' | use ''BLASTDB=/export/data/bio/uniprot/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'' 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''
biological-databases.txt · Last modified: 2023/10/09 11:18 by aorth