[Bioperl-l] SeqHound

Brian Osborne bosborne11 at verizon.net
Tue Sep 9 10:50:38 EDT 2008


Raul,

After spending a few minutes at bond.unleashedinformatics.com I have  
to admit that it's not clear how one accesses their free version of  
BOND. There are no examples that I can see in their packages.

If you are interested in looking at protein-protein networks in the  
Bioperl context you can also check out the bioperl-network package:

http://www.bioperl.org/wiki/Network_package

If you don't care what language you're using then you should consider  
Cytoscape, it's probably the package with the most capability.


Brian O.


On Sep 3, 2008, at 10:33 AM, Raul Mendez Giraldez wrote:

> Hi Chris,
>
> I'm trying to set up and run bioperl Seqhound donwloaded from:
>
> http://bond.unleashedinformatics.com/downloads/api//seqhound-bioperl-4.0.tar.gz
>
> and I always get connection error messages. Do you know which  
> version of
> SeqHound should I use and how can I configure to make it work? I've
> tried several possibilities for server1 at .shoundremrc as
>
> [remote]
> server1 = bond.unleashedinformatics.com
> CGI = /cgi-bin/seqrem
> port=8080
>
> Also, I would like to get all the possible protein-protein interaction
> for a set of protein sequences. Would this be possible using SeqHound?
>
> Thanks,
> Raúl
>
>
>
>
> -- 
> Raúl Méndez Giráldez, Ph.D.
> Bioinformatics Unit
> Centre for Molecular Biology "Severo Ochoa"
> Universidad Autónoma de Madrid
> C/ Nicolás Cabrera, 1
> Cantoblanco 28049, Madrid
> SPAIN
>
> Phone: +34 91 196 4633
>
>
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> Bioperl-l at lists.open-bio.org
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