[Bioperl-l] Fwd: SeqHound

Barry Moore barry.moore at genetics.utah.edu
Wed Feb 6 16:50:53 EST 2008


Susan-

Yeah, I used them several  years ago, and it seemed like quite a good  
project at the time.  I see that it has recently moved to a new  
location with a start up company, and I couldn't make heads or tails  
of their new sight.  I wonder if the SeqHound side of their work  
hasn't suffered - perhaps only temporarily - from their recent move  
from academia to the brave new world of .com start-up.

B

On Feb 6, 2008, at 1:57 PM, Susan J. Miller wrote:

> 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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