[BioPython] comparing short sequences against genome

[Malcolm Cook]

and look at ssaha and blat (which has bioperl wrapper)

"bartek wilczynski" <bartek at rezolwenta.eu.org> wrote in message
news:1096331400.4158b088afaf6 at imp.rezolwenta.eu.org...
> Citing Bzy Bee <nomy2020 at yahoo.com>:
> <cut>
> > What I have been unable to do so far is:
> >
> > 1) the oligos (both forward and reverse) to iterate
> > through the entire file, i.e. each and every sequence
> > in the file (and keeping track of sequence names and
> > positions when a match is found). At the moment it
> > just takes the first 10 mers of sequence 1 (and 10
> > mers at position 290) and compares these with sequence
> > 1, but not with sequence 2 and 3 and so on
> >
> > 2) secondly, I want to add one to the starting
> > position of 10 mers, i.e. in the second round of
> > iteration, instead of taking:
> >      oligoF = result[0:10]
> > it should take result[1:11], i.e. increasing the
> > position of 10 mer by 1 (and same for reverse oligo)
> > and so on until teh sequence finishes. I'm not sure
> > how to increment the result by 1.
> >
> > I am kinda stuck at both these steps and any help
> > would be very much appreciated.
> <cut a lot>
>
> Hi,
>
> I've attached modified version of your program that does what you want.
It's not
> clean and it's not even nearly as fast as it needs to be if you are
thinking
> about genomic scale experiments.
>
> If you need to just do this once and not for very long sequences, you can
use
> this. Otherwise, I would recommend reading something about suffix trees.
> HOnestly I don't know if there's any code related to that in biopython.
>
> regards
>
> Bartek Wilczynski
>


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