[Bioperl-l] from protein to nucleotide

Jack Chen chenn at cshl.edu
Fri Jun 13 10:52:57 EDT 2003


Here is another question about GenBank sequence object. I am wondering
whether there is a convenient way to retrieve the nucleotide sequence of a
protein with known gi number. For example, for protein
gi|497063|gb|AAB60473.1|, how should I get its corresponding nucleotide?
Manually, I can get it by visiting the NCBI page and follow the links. But
is there a way to do this automatically?

Also, does anyone know how to parse the GenPept sequence object to get the
'DBSOURCE' field? For example, how can I get the accession number
'U05729.1' from the following record? Thanks!

LOCUS       AAB60473                  39 aa            linear   ROD
DEFINITION  preproinsulin I.
VERSION     AAB60473.1  GI:497063
DBSOURCE    locus MSU05729 accession U05729.1
SOURCE      Mus spretus (western wild mouse)
  ORGANISM  Mus spretus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
            Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae;


|    o-o     Jack Chen, Stein Laboratory       |
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