[Bioperl-l] obtaining nt seqs using protein GI's

Jason Stajich jason.stajich at duke.edu
Fri Apr 8 13:25:47 EDT 2005

% formatdb -o T -i nt -p F
% fastacmd -i FILEWITHGIs -d nt

Jason Stajich
jason.stajich at duke.edu

On Apr 8, 2005, at 11:43 AM, Nathan Spencer Haigh wrote:

> This must have been done a million times, but i haven't got time at 
> the moment
> to find out the answer myself.
> I have a list of GI's for which i would like to obtain the nucleotide 
> sequences
> (including introns); can anyone give me some pointers?
> What i'm trying to do is this: i've used blastclust on ~5000 protein 
> sequences
> to identify those with high sequence identity at the aa level, now i 
> would like
> to create an alignment of the same sequences using nt and if possible 
> include
> introns to try and identify any sequence variations.
> Thanks
> Nathan
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