[Biopython] blastall - strange results

[Peter]

On Thu, May 28, 2009 at 1:02 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> 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?

I would check the filtering option is off (by default BLAST will mask low
complexity regions).

> 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

Brad is probably right about normal BLAST not being the best tool.

However, if you haven't done so already you might want to try
megablast instead of blastn, as this is designed for very similar
matches. This should be a very small change to your existing Biopython
script, so it should be easy to try out.

Peter