[Bioperl-l] PDB sequence from ATOM records
Matthew.Betts at ii.uib.no
Thu Jul 1 10:50:46 EDT 2004
I need to be able to map some protein sequence alignment information on to
a protein structure. To do this I need to get the sequence from the ATOM
records, since the SEQRES sequence is often not exactly the same.
So I'd like to change Bio::Structure::Residue a little:
Amino-acid type and residue number are currently contained in one value,
residue->id. I would like to separate them in to two, residue->type
and residue->num. Then, for backwards compatibility, construct residue->id
from these each time it is required (or store it as well if that is
better?). residue->type should be able to return the one-letter code as
well as the three-letter code.
And then have a method called something like Bio::Structure::Entry->atom_seq
that would return a Bio::PrimarySeq object constructed from the one-letter
codes of the residues of a particular chain.
Any comments please... Thanks.
P.S. Sorry if this message is a repeat - our email server went down as I
was sending it the first time.
Matthew Betts, mailto:matthew.betts at ii.uib.no
Phone: (+47) 55 58 40 22, Fax: (+47) 55 58 42 95
CBU, BCCS, HiB, UNIFOB / Universitetet i Bergen
Thormøhlensgt. 55, N-5008 Bergen, Norway
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