<p>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.</p>

<p>Here is an eample of simple query to the Nucleotide collection database using &quot;blastn&quot; algorithm.</p>

<pre>
<code>from Bio.Blast import NCBIWWW

result_handle = NCBIWWW.qblast(&quot;blastn&quot;, &quot;nt&quot;, some_sequence)
</code></pre>

<p>As you can see, the database Nucleotide collection is specified as &quot;nt&quot;. With what shall I substitute &quot;nt&quot; 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 <a href="http://blast.ncbi.nlm.nih.gov">http://blast.ncbi.nlm.nih.gov</a> ?</p>

<p>Thanks!</p>

This is [the list of preformatted BLAST databases available at BLAST FTP site][1].

I parsed the list and tested these databases with a script. All of them work except 3.

**Protein databases**

```
env_nr
nr
pataa
pdbaa
refseq_protein
swissprot
```

**Non-RefSeq nucleotide databases**

```
env_nt
est
est_human
est_mouse
est_others
gss
htgs
nt
patnt
pdbnt
sts
vector
wgs
```

**RefSeq nucleotide databases**

```
human_genomic #obsolete, renamed to refseq_genomic_human
human_genomic_transcript #obsolete
mouse_genomic_transcript #obsolete
other_genomic
refseq_genomic
refseq_rna
refseqgene #obsolete
```

To your second question about how to search against an older human genome build (Human GRCh37/hg19), I am afraid you cannot do it with remote BLAST. You need to download [the older data][2] and create a BLAST database and run BLAST locally.

 [1]: http://www.ncbi.nlm.nih.gov/books/NBK62345/#_blast_ftp_site_The_blastdb_subdirectory_
 [2]: ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/