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Nucleic Acids Research Advance Access originally published online on October 21, 2008
Nucleic Acids Research 2009 37(Database issue):D571-D578; doi:10.1093/nar/gkn744
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Nucleic Acids Research, 2009, Vol. 37, Database issue D571-D578
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics

John Martin, Sahar Abubucker, Todd Wylie, Yong Yin, Zhengyuan Wang and Makedonka Mitreva*

The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA

*To whom correspondence should be addressed. Tel: +1 314 286 1118; Fax: +1 314 286 1810; Email: mmitreva{at}watson.wustl.edu

Received August 8, 2008. Revised September 19, 2008. Accepted October 3, 2008.

Nematode.net (http://nematode.net) is a publicly available resource dedicated to the study of parasitic nematodes. In 2000, the Genome Center at Washington University (GC) joined a consortium including the Nematode Genomics group in Edinburgh, and the Pathogen Sequencing Unit of the Sanger Institute to generate expressed sequence tags (ESTs) as an inexpensive and efficient solution for gene discovery in parasitic nematodes. As of 2008 the GC, sampling key parasites of humans, animals and plants, has generated over 500 000 ESTs and 1.2 million genome survey sequences from more than 30 non-Caenorhabditis elegans nematodes. Nematode.net was implemented to offer user-friendly access to data produced by this project. In addition to sequence data, the site hosts: assembled NemaGene clusters in GBrowse views characterizing composition and protein homology, functional Gene Ontology annotations presented via the AmiGO browser, KEGG-based graphical display of NemaGene clusters mapped to metabolic pathways, codon usage tables, NemFam protein families which represent conserved nematode-restricted coding sequences not found in public protein databases, a web-based WU-BLAST search tool that allows complex querying and other assorted resources. The primary aim of Nematode.net is the dissemination of this diverse collection of information to the broader scientific community in a way that is useful, consistent, centralized and enduring.


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