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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<title> www.nematodes.org - NEMBASE4 </title>
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<div class="mainTitle">
<div align="left">What is NEMBASE4?</div>
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<p>
NEMBASE is a resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design. </p>
<p>NEMBASE4 was constructed by Ben Elsworth using the PartiGene suite of tools, with assistance from James Wasmuth and Mark Blaxter.<br>
Any questions, please contact <a href="mailto:[email protected]">Mark Blaxter</a>. <br>
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<div class="mainTitle">
Searching NEMBASE4 and retrieving data
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<p>You can search NEMBASE4 using the links on the navigation bar to the left.<br>
To download NEMBASE4 datasets click <a href="/downloads/databases/NEMBASE4/index.shtml" target="_top">here</a> <br>
To download PartiGene and other software click <a href="../bioinformatics/index.shtml" target="_top">here</a>.</p>
<div class="mainTitle">
NEMBASE4: Current Status
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<p><blockquote>
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<a href="nembase4contents.shtml">See here for a data summary by species, and sources of data. </a> <br>
<a href="overview.shtml" target="_top">Click here for Species Specific Information.</a>
<br>
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<div class="mainTitle">
NEMBASE Publications
</div>
<blockquote>
<p>
<a href="http://www.sciencedirect.com/science/article/pii/S0020751911001044"><span class="style1">JUST PUBLISHED</span> NEMBASE4: The nematode transcriptome resource (open access article)</a><br>
Benjamin Elsworth, James Wasmuth and Mark Blaxter. International Journal for Parasitology Volume 41, Issue 8, July 2011, Pages 881-894 </p>
<p><a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2432500">On the Extent and Origins of Genic Novelty in the Phylum Nematoda.</a>
<br>
Wasmuth J, Schmid R, Hedley A, Blaxter M. PLoS Neglected Tropical Diseases (2008). Jul 2(7):e258.</p>
<p><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=A transcriptomic analysis of the phylum Nematoda">A transcriptomic analysis of the phylum Nematoda</a>.<br>
Parkinson, J., M. Mitreva, et al. (2004). Nature Genetics 36(12): 1259-67.</p>
<p><a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14681449">
NEMBASE: a resource for parasitic nematode ESTs.</a>
<br>
Parkinson J, Whitton C, Schmid R, Thomson M, Blaxter M. (2004). Nucleic Acids Res. 32(Database issue):D427-30.<br>
This previous release is still available at <a href="http://www.nematodes.org/nembase3/">NEMBASE3</a><br>
</p>
</blockquote>
<p>NEMBASE4 is built using the PartiGene Suite of EST analysis tools:</p>
<blockquote>
<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=14988115&query_hl=1&itool=pubmed_docsum">PartiGene--constructing partial genomes.</a>
<br>
Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, Blaxter M. (2004). Bioinformatics 20:1398-404. Epub 2004 Feb 26.</p>
<p><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=prot4EST%3A translating expressed sequence tags from neglected genomes.">prot4EST: Translating Expressed Sequence Tags from neglected genomes</a><br>
Wasmuth, J. D. and M. L. Blaxter (2004). BMC Bioinformatics 5: 187.</p>
<p><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=Making sense of EST sequences by CLOBBing them">Making sense of EST sequences by CLOBBing them</a><br>
Parkinson, J., D. B. Guiliano, et al. (2002). BMC Bioinformatics 3: 31. </p>
<p><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=400000 nematode ESTs on the Net">400000 nematode ESTs on the Net</a>.<br>
Parkinson, J., M. Mitreva, et al. (2003). Trends Parasitol 19: 283-6. </p>
<p><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=200000 nematode expressed sequence tags on the Net">200000 nematode expressed sequence tags on the Net</a><br>
Parkinson, J., C. Whitton, et al. (2001). Trends Parasitol 17: 394-396.</p>
</blockquote>
<div class="mainTitle">Other Nematode Genomics Sites </div>
<table>
<tr>
<td><div align="right"><a href="http://www.nematode.net/" target="_blank"><img src="/images/nematode_net.png" width="355" height="42"></a></div></td>
<td>Our sister site, <a href="http://www.nematode.net/" target="_blank">nematode.net</a>, at the University of Washington Genome Sequenciung Centre, also offers nematode EST analyses.</td>
</tr>
<tr>
<!--td><img src="http://www.wormbase.org/images/image_new_colour.jpg" width="355" height="42"></td-->
<td><a href="http://www.wormbase.org/" style="text-decoration: none" target="_blank"><font size="5"> <b>WormBase</b></font></a></td></div>
<td>The <em>Caenorhabditis elegans, Caenorhabditis briggsae, Caenorhabditis remanei</em> and <em>Brugia malayi</em> genomes are browsable through WormBase <a href="http://www.wormbase.org">http://www.wormbase.org</a></td>
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<p align="center">NEMBASE is maintained by Mark Blaxter</p>
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