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

[Mingwei Min]

Many thanks, Chris, that's exactly what I need.

Mingwei

2011/2/21 Chris Fields <cjfields at illinois.edu>:
> If this is a direct string match (no ambiguity), just use perl's index function:
>
>       index STR,SUBSTR,POSITION
>       index STR,SUBSTR
>               The index function searches for one string within another, but
>               without the wildcard-like behavior of a full regular-expression
>               pattern match.  It returns the position of the first occurrence
>               of SUBSTR in STR at or after POSITION.  If POSITION is omitted,
>               starts searching from the beginning of the string.  POSITION
>               before the beginning of the string or after its end is treated
>               as if it were the beginning or the end, respectively.  POSITION
>               and the return value are based at 0 (or whatever you've set the
>               $[ variable to--but don't do that).  If the substring is not
>               found, "index" returns one less than the base, ordinarily "-1".
>
> Also see here:
>
> http://perlmeme.org/howtos/perlfunc/index_function.html
>
> chris
>
> On Feb 20, 2011, at 4:28 PM, Mingwei Min wrote:
>
>> 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
>>>>>
>>>>>
>>>
>>>
>>
>>
>>

>>
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