What is NEMBASE4?

NEMBASE is a resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design.

NEMBASE4 was constructed by Ben Elsworth using the PartiGene suite of tools, with assistance from James Wasmuth and Mark Blaxter.
Any questions, please contact Mark Blaxter.

Searching NEMBASE4 and retrieving data

You can search NEMBASE4 using the links on the navigation bar to the left.
To download NEMBASE4 datasets click here
To download PartiGene and other software click here.

NEMBASE4: Current Status

Number of Species	62
Number of Libraries &nbsp&nbsp	324
Number of Clusters	237,181
Number of ESTs	679,480

See here for a data summary by species, and sources of data.
Click here for Species Specific Information.

NEMBASE Publications

JUST PUBLISHED NEMBASE4: The nematode transcriptome resource (open access article)
Benjamin Elsworth, James Wasmuth and Mark Blaxter. International Journal for Parasitology Volume 41, Issue 8, July 2011, Pages 881-894

On the Extent and Origins of Genic Novelty in the Phylum Nematoda.
Wasmuth J, Schmid R, Hedley A, Blaxter M. PLoS Neglected Tropical Diseases (2008). Jul 2(7):e258.

A transcriptomic analysis of the phylum Nematoda.
Parkinson, J., M. Mitreva, et al. (2004). Nature Genetics 36(12): 1259-67.

NEMBASE: a resource for parasitic nematode ESTs.
Parkinson J, Whitton C, Schmid R, Thomson M, Blaxter M. (2004). Nucleic Acids Res. 32(Database issue):D427-30.
This previous release is still available at NEMBASE3

NEMBASE4 is built using the PartiGene Suite of EST analysis tools:

PartiGene--constructing partial genomes.
Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, Blaxter M. (2004). Bioinformatics 20:1398-404. Epub 2004 Feb 26.

prot4EST: Translating Expressed Sequence Tags from neglected genomes
Wasmuth, J. D. and M. L. Blaxter (2004). BMC Bioinformatics 5: 187.

Making sense of EST sequences by CLOBBing them
Parkinson, J., D. B. Guiliano, et al. (2002). BMC Bioinformatics 3: 31.

400000 nematode ESTs on the Net.
Parkinson, J., M. Mitreva, et al. (2003). Trends Parasitol 19: 283-6.

200000 nematode expressed sequence tags on the Net
Parkinson, J., C. Whitton, et al. (2001). Trends Parasitol 17: 394-396.

Other Nematode Genomics Sites

	Our sister site, nematode.net, at the University of Washington Genome Sequenciung Centre, also offers nematode EST analyses.
��WormBase	The Caenorhabditis elegans, Caenorhabditis briggsae, Caenorhabditis remanei and Brugia malayi genomes are browsable through WormBase http://www.wormbase.org

NEMBASE is maintained by Mark Blaxter