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

[rich]

ah, yes, not sure how to get around this.....

Quoting Iddo <idoerg at burnham.org>:

> 
> 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
> 
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