[Biopython] blastall - strange results
Stefanie Lück
lueck at ipk-gatersleben.de
Thu May 28 07:55:30 UTC 2009
Hi!
The question is not really related to a biopython problem but nevertheless I
want to be sure that I do everything correct.
I get strange results with blast.
My aim is to blast a query sequence, spitted to 21-mers, against a database.
Since I need only 100 % matches of 21-mers, a set the word size parameter to
21. Now, as a positive control, I took one EST sequence and made a database
of it. Then I took 100 bp of that sequence, spitted to 21-mers and blast
each of them against my DB.
Now I expect to get a full coverage (or better 80 hits because everything
below 21 bp I don't blast) of hits because the sequence is fully present in
the DB. Unfortunately blast finds much less (60-80 %, depending on the
sequence).
Is this normal? I would expect to find all 21-mers. Why only some?
If I blast without to change the word size parameter its find all hits. But
I would like to use this parameter because the blast is much faster and I
don't need to take care about gaps etc. since I really need only 100 % 21
mer matches.
Does someone have any ideas what could be the problem?
Thanks in advance!
Stefanie
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