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[Bio-software] Please recommend good ontology analysis tools

Robert Miles via bio-soft%40net.bio.net (by milesrf from usenet-news.net)
Sat Jul 31 10:21:13 EST 2010


"RY Bao" <ry_bao from yahoo.com> wrote in message 
news:mailman.936.1280460013.25217.bio-soft from net.bio.net...
> Hello Everybody,
>
> I have a list of about 6000 genes, with around 800 of them associated with 
> gene
> family expansion. I want to detect GO over/under-representation in this 
> dataset.
> I have tried GOstat (FDR Benjamini), GOToolBox (Hypergeometric, Benjamini 
> &
> Hochberg), and Ontologizer (Parent-Child-Union, Benjamini-Hochberg). 
> However,
> they gave me very different results. Could anybody give me some 
> suggestions
> about which program to use, or which model gives better results? Are there 
> any
> other recommended programs that I can use? Thank you so much! :-)
>
> Greetings,
> Sunny Bao (Wayne State University, US)

I've found two BOINC projects associated with genetic research, but not
the corresponding ways to submit work for them to do.

http://cbl-boinc-server2.cs.technion.ac.il/superlinkattechnion/
Located in Israel; mostly human genetic research.

http://boinc.bio.wzw.tum.de/boincsimap/
Located in Germany; mostly comparisons of protein sequences
from different species, but also some comparisons of genetic
sequences from different species.

I've seen little sign that either of them will make their software
available for use elsewhere.

Robert Miles 



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