NEMBASE: a resource for parasitic nematode ESTs.
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 approximately 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.
Parkinson
John
J
Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King's Buildings, West Mains Road, University of Edinburgh, Edinburgh EH9 3JT, UK. jparkin@sickkids.ca
Whitton
Claire
C
Schmid
Ralf
R
Thomson
Marian
M
Blaxter
Mark
M
D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D017238:Genes, Helminth; D016678:Genome; D023281:Genomics; D016247:Information Storage and Retrieval; D020407:Internet; D009348:Nematoda / Q000145:classification / Q000235:genetics*; D010271:Parasites / Q000235:genetics*