[Bioperl-l] question about positioning peptide in a full protein sequence

[Dave Messina]

Hi Mingwei,

Please remember to "reply all" so others on the mailing list can follow the
conversation.

Unless you have some way of other way of mapping the coordinates of the
sequence with the post-translational sites to the coordinates of the full
sequence, I think you'll have to do a similarity search of some form.

BLAST may not be best for this, given that it's sloppy with the ends of an
alignment, but there are plenty of options for BLAST that may improve your
results. Again, you'll need to be specific about your problem for us to
help. I don't what "too complex for this simple job" means. Is it too slow?
Are you getting too many hits?



Dave



On Sun, Feb 20, 2011 at 22:35, Mingwei Min <mm809 at cam.ac.uk> wrote:

> Hi Dave,
>
> Sorry for not making it clear. Yes, I just want to get the coordinates
> of the post-translational sites out of a protein sequence. And what I
> have now is the peptide sequence with marker on the post-translated
> residue... what should i do to map them to the whole protein sequence
> and get the coordinates? The only way I could come up with is blast.
> But it seems to be too complex for this simple job....
>
> Many thanks,
>
> Mingwei
>
> 2011/2/20 Dave Messina <David.Messina at sbc.su.se>:
> > Hi Mingwei,
> > I'm not sure what you mean by "positioning" here. Do you want to get the
> > coordinates of the post-translational sites out of a protein sequence
> > database record? Or do you want to draw the post-translational sites on a
> > picture of the protein sequence? Or something else entirely?
> >
> > Dave
> >
> >
> >
> > On Sat, Feb 19, 2011 at 15:53, Mingwei Min <mm809 at cam.ac.uk> wrote:
> >>
> >> Hi,
> >>
> >> I am trying to positioning some post-tranlational modification sites,
> >> which is marked in peptides, in a full length protein sequence. Anyone
> >> would be kind to tell me the model I could use for this?
> >>
> >> Many thanks
> >>
> >> Mingwei
> >> _______________________________________________
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> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>