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Nucleic Acids Research, 2004, Vol. 32, Database issue D427-D430
© 2004 Oxford University Press

NEMBASE: a resource for parasitic nematode ESTs

John Parkinson*, Claire Whitton, Ralf Schmid, Marian Thomson and Mark Blaxter

Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King’s Buildings, West Mains Road, University of Edinburgh, Edinburgh EH9 3JT, UK

*To whom correspondence should be addressed at present address: Programs in Genetics and Genomic Biology/Structural Biology and Biochemistry, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada. Tel: +1 416 813 7654 ext. 1457; Fax: +1 416 813 5022; Email: jparkin{at}sickkids.ca

NEMBASE (available at http://www.nematodes.org) is a publicly available online database providing access to the sequence and associated meta-data currently being generated as part of the Edinburgh–Wellcome Trust Sanger Institute parasitic nematode EST project. NEMBASE currently holds ~100 000 sequences from 10 different species of nematode. To facilitate ease of use, sequences have been processed to generate a non-redundant set of gene objects (‘partial genome’) for each species. Users may query the database on the basis of BLAST annotation, sequence similarity or expression profiles. NEMBASE also features an interactive Java-based tool (SimiTri) which allows the simultaneous display and analysis of the relative similarity relationships of groups of sequences to three different databases. NEMBASE is currently being expanded to include sequence data from other nematode species. Other developments include access to accurate peptide predictions, improved functional annotation and incorporation of automated processes allowing rapid analysis of nematode-specific gene families.


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