BLAST via Biopython NCBIWWW. Where can I find the complete database list?
Question: I am using the module Biopython module NCBIWWW to blast some sequences online.
I would like to blast my sequences against different databases available,
however I cannot find a comprehensive list of them.

Here is an eample of simple query to the Nucleotide collection database using
"blastn" algorithm.

    
    
    from Bio.Blast import NCBIWWW
    
    result_handle = NCBIWWW.qblast("blastn", "nt", some_sequence)
    

As you can see, the database Nucleotide collection is specified as "nt". With
what shall I substitute "nt" in case I want to query the Human GRCh37/hg19
database for example? And if I want to query other species/builds? Is there
any comprehensive list available where I can find the short names for all the
databases available at <http://blast.ncbi.nlm.nih.gov> ?

Thanks!


Answer: You can simply go to
[http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome)
and click on the database drop down list and you will find the database names
there like, nr, nt, est etc.

Try
[http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&BLAST_SPEC=OGP__9606__9558](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&BLAST_SPEC=OGP__9606__9558)
for Human Genome.

