Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

Automated EST - GO mapping

Mark E. Waugh mew at ncgr.org
Thu Feb 5 13:31:06 PST 2004


Hi Chris,

We have developed an EST/genomic analysis pipeline that, in the case of 
ESTs cleans the data, clusters and assembles it and, in both cases, 
performs a number of configurable analysis and annotation operations 
including BLASTX vs. nr, BLIMPS searches against the Blocks+ motif 
database, and uses some or all of the 11 or so algorithms in 
InterProScan against InterPro. It also performs PexFinder searches for 
excreted proteins (an  algorithm developed in conjunction with Ohio 
State as part of our ongoing work with Phytophthora spp.). The results 
include automated GO assignments based on SWISS PROT to GO mappings 
(based on features with SP entries) as well as the GO assignments 
included in InterPro through their curation effort. The results are 
visualized through a web interface, examples of which can be found at 
www.pfgd.org, www.solgd.org or our latest project, the Legume 
Information System at www.comparative-legumes.org. The core sequence 
analysis component comprises a relational database, an analysis and 
annotation pipeline written in Java that does distributed processing 
through RMI, and a web component based on Apache. The system is known 
as XGI (X Genome Initiative) and is available for non-commercial use 
for nominal shipping and handling charges. Feel free to contact myself 
directly or see http://www.ncgr.org/xgi for more details.

Hope this helps,

Mark


On Thursday, February 5, 2004, at 01:42 PM, Chris Beck wrote:

> Hi,
>
> Our project is using high throughput processes to generate complete 
> coverage cDNA libraries of several dozen fungal species.  I'm new to 
> the whole field but I'm hoping that some of you are involved in this 
> whole high throughput genomics thing as well.
>
> We'd like to automatically associate GO terms with our various fungal 
> ESTs/Clusters/Contigs using InterProScan and BLAST->SwissProt/TrEMBL 
> dbs and have 2-way browsing (find ESTs by GO term, find GO terms by 
> EST, show pretty tables).  I was wondering if any of you had run 
> across automated processes that can annotate your info.  Obviously 
> running the sequences against the dbs is straight forward but there 
> are some interesting decisions to make respecting confidence levels 
> and conflicting results as well as presentation that have probably 
> been done before and we're trying to figure out what the 
> best-practices approach is.  Any suggestions?
>
> Cheers,
> Chris
>
> -- 
> Chris Beck / Y.A.B.A. / Fungal Genomics	/ CFSG / Concordia University
> "Opinions of bureaucrats do not create wrongs"
>
>
> --
> This message is from the GOFriends moderated mailing list.  A list of 
> public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: 
> owner-gofriends at geneontology.org
> Subscribing   send   "subscribe"   to   
> gofriends-request at geneontology.org
> Unsubscribing send   "unsubscribe"  to  
> gofriends-request at geneontology.org
> Web:          http://www.geneontology.org/
>
>
Mark Waugh, Group Leader, Bioinformatics
The National Center for Genome Resources
2935 Rodeo Park Drive East
Santa Fe, NM 87505 U.S.A.
voice: (505) 995-4446
fax: (505) 995-4432


--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list