[Biopython] (no subject)

[Tanya Golubchik]

Wouldn't it be faster to pre-check for a perfect match using a python
string function?

if primer_seq in genome_seq:
    return MatchFound
else:
    <do blast>

Cheers,
Tanya


On 14/04/12 12:41, Matthias Schade wrote:
> Hello everyone,
> 
> 
> I would like to run a blastn-query of a small nucleotide-sequence
> against a genome. The code works already, but my queries are still slow
> and mostly ineffective, so I would like to ask:
> 
> Is there a way to tell the blastn-algorithm that once a 'perfect match'
> has been found it can stop and send back the results?
> 
> Background: I am interested in only the first full match because I would
> like to design a nucleotide-probe which -if possible- has no(!) known
> match in a host-genome, neither in RNA nor DNA. Actually, I would reject
> all perfect-matches and all single-mismatches but allow every sequence
> with two or more mismatches.
> 
> Currrently, I use this line of code with seq_now being about 15-30 nt long:
> result_handle = NCBIWWW.qblast("blastn", "nt", seq_now,
> entrez_query="Canis familiaris[orgn]")
> 
> 
> I am still new to this. Thank you for your help and input,
> 
> Matt
> 
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