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

[Mingwei Min]

Hi Dave,

Thank you for your suggestion. when I said "too comple for this simple
job", I just thought that there might be some particular module that
could do this straightforwardly. I'll have a try of BLAST anyway.
Thank you.

Mingwei

2011/2/20 Dave Messina <David.Messina at sbc.su.se>:
> 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
>> >> _______________________________________________
>> >> Bioperl-l mailing list
>> >> Bioperl-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>> >
>
>



-- 
Mingwei Min  PhD student
University of Cambridge
Department of Genetics
Downing St
CB2 3EH
UK