NEMBASE: a resource for parasitic nematode ESTs

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

Research output: Contribution to journalArticlepeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)D427-30
JournalNucleic Acids Research
Volume32
Issue numberDatabase issue
DOIs
Publication statusPublished - 2004

Keywords

  • Animals
  • Computational Biology
  • Databases, Genetic
  • Expressed Sequence Tags
  • Gene Expression Profiling
  • Genes, Helminth
  • Genome
  • Genomics
  • Information Storage and Retrieval
  • Internet
  • Nematoda
  • Parasites

Fingerprint Dive into the research topics of 'NEMBASE: a resource for parasitic nematode ESTs'. Together they form a unique fingerprint.

Cite this