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

rich dobbo at thevillas.eclipse.co.uk
Thu Jul 15 05:24:10 EDT 2004


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
> >_______________________________________________
> >BiO_Bulletin_Board maillist  - 
> BiO_Bulletin_Board at bioinformatics.org
>
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
> >
> >  
> >
> 
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