[Biopython] blastall - strange results

[Brad Chapman]

Hi Stefanie;

> I get strange results with blast.
> My aim is to blast a query sequence, spitted to 21-mers, against a database.
[...]
> Is this normal? I would expect to find all 21-mers. Why only some?

BLAST isn't the best tool for this sort of problem. For exhaustively
aligning short sequences to a database of target sequences, you
should think about using a short read aligner. This is a nice
summary of available aligners:

http://www.sanger.ac.uk/Users/lh3/NGSalign.shtml

Personally, I have had good experiences using Mosaik and Bowtie.

Hope this helps,
Brad