[Bioperl-l] SeqHound

Susan J. Miller sjmiller at email.arizona.edu
Wed Feb 6 15:57:35 EST 2008


Barry Moore wrote:
> Susan,
> 
> I'm joining this discussion late so my apologies if I'm missing the 
> original point.  If you're trying to routinely download thousands of 
> sequences from GenBank or SeqHound you probably want to be using ftp to 
> download the flat files and query/parse locally.  If you're trying to 
> stay on top of the latest Drosophila ESTs, then how about setting up a 
> nightly cron job to download the incremental updates from NCBIs ftp 
> (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for Drosophila 
> EST sequences.  The EST division is huge, but I would think nightly 
> incrementals should be manageable.


Hi Barry,

I'll try your suggestion.  I guess my interpretation of the 
documentation for SeqHound was erroneous.  (Who knows what 'large 
numbers of sequences' means?)  I tried using SeqHound's get_Stream_by_id 
method to fetch 10000 sequences, 500 at a time, and got a timeout error.


-- 
Regards,
-susan

Susan J. Miller
Manager, Scientific Data Analysis
Biotechnology Computing Facility
Arizona Research Laboratories
(520) 626-2597


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