[BiO BB] mapping swissprot sequence positions to pdb sequence positions

[Iddo]

Sounds pretty good. Going through the hssp seqno would be my choice too.
Be aware that the gaps are marked with a "!", and I _think_ those "!"s
are numbered too. (To lazy to look at an HSSP file now).

Good luck,

Iddo


rich wrote:

>Hi, yes, thanks. I was thinking about using Align. I am
>using hssp entries which have a consecutive seqno
>position. I want to map these values onto the position
>within the swissprot entry for the protein sequence. I
>realise that there will be gaps etc in the pdb num but
>there won't be in the hssp seqno values.
>
>effectively i have snps and their positions and i want
>to map onto the seqno value from the hssp file. The
>seqno value is simply a consecutive seq position as
>opposed to the pdb seq position.
>
>I think the solution is to run Align on all of my
>sequences and then parse with Bio::Align, unless there
>is a quicker way that I haven't thought of
>
>cheers
>Rich
>
>thanks
>Rich
>
>Quoting Iddo Friedberg <idoerg at burnham.org>:
>
>  
>
>>A pairwise alignment program, such as blast2seq
>>or EMBOSS's "needle" is 
>>probably good for you.
>>
>>I'm not sure I understand your question, is the
>>sequence position coming 
>>from the SwissProt file or from the PDB? If the
>>latter, be aware that:
>>
>>1) PDB sequences contain gaps.
>>2) Sequence numbers in PDB are non-consecutive
>>even if there are no gaps.
>>3) Sequence numbering can be alphanumeric and
>>contain insertion 
>>codes(e.g. 183, 183A, 183B, 184)
>>4) Sequecnes can start with negative numbers
>>(e.g. for his-tagged proteins)
>>5) Mutations abound.
>>
>>Iddo
>>
>>rich wrote:
>>
>>    
>>
>>>Hi,
>>>
>>>could anyone recommend a quick way of mapping
>>>      
>>>
>>the
>>    
>>
>>>positions in say a swissprot peptide sequence
>>>      
>>>
>>file onto
>>    
>>
>>>the pdb sequence file? I want to know the
>>>      
>>>
>>actual
>>    
>>
>>>sequence position values.
>>>
>>>thanks
>>>rich
>>>_______________________________________________
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-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo