Differences

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--- biological-databases [2019/03/13 19:49] – aorth
+++ biological-databases [2019/03/13 20:11] – aorth
@@ Line 5: / Line 5: @@
 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              ^Database Location          ^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 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 |
@@ Line 12: / Line 12: @@
 | UniProt's UniRef100 | N/A | ? | ''/export/data/bio/uniprot/blast/db'' | use ''BLASTDB=/export/data/bio/uniprot/blast/db'' in your Bash script |
-==== Footnotes ====
+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'':
+<code>
+$ export BLASTDB=/export/data/bio/ncbi/blast/db
+$ blastn -db nt -query file.seq -out blast.out
+</code>
+<html>
+<hr />
+</html>
 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''