[Bioperl-l] Get nucleotide sequence when expecting proteinfromgenpept

[Frederick Partridge]

On Tue, 11 Jul 2006, Chris Fields wrote:
> This returns both the nucleotide sequence and the correct protein sequence;
> the protein was returned second for some reason, so get_Seq_by_acc misses it
> while get_Stream_by_acc doesn't.  I have notified NCBI about this issue, but
> they will likely just tell me to use the GI number for searches as they are
> unique.  Probably a good warning for anyone using accessions for all their
> work (I use the GI myself).


Thank you both for your help, I have converted to GIs and it works much
better.

As an aside, it might be nice to have a $hit->gi method as well as
$hit->accession for parsing blast reports. (I now realise that you can
derive the gi from $hit->name, but this might have encouraged me to start
off using gi instead of accession numbers).


Freddie Partridge

University of Oxford