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

Iddo Friedberg idoerg at burnham.org
Wed Jul 14 19:44:12 EDT 2004

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.


rich wrote:

>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.
>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org

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