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NEMBASE: a resource for parasitic nematode ESTs.

John Parkinson1, Claire Whitton, Ralf Schmid

  • 1Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King's Buildings, West Mains Road, University of Edinburgh, Edinburgh EH9 3JT, UK. jparkin@sickkids.ca

Nucleic Acids Research
|December 19, 2003
PubMed
Summary

NEMBASE is a free online database offering over 100,000 sequences from 10 nematode species. It aids researchers in analyzing parasitic nematode gene data and expression profiles.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Parasitology

Background:

  • Parasitic nematodes pose significant threats to agriculture and human health.
  • Understanding nematode genetics is crucial for developing effective control strategies.
  • The Edinburgh-Wellcome Trust Sanger Institute parasitic nematode EST project generates extensive sequence data.

Purpose of the Study:

  • To introduce NEMBASE, a comprehensive online database for parasitic nematode sequence data.
  • To provide researchers with a user-friendly platform for accessing and analyzing nematode genetic information.
  • To support the ongoing research efforts in parasitic nematode genomics.

Main Methods:

  • Compilation and processing of approximately 100,000 expressed sequence tags (ESTs) from 10 nematode species.

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  • Generation of non-redundant gene objects representing a partial genome for each species.
  • Development of query functionalities based on BLAST annotation, sequence similarity, and expression profiles.
  • Implementation of an interactive Java-based tool (SimiTri) for simultaneous analysis of sequence similarity relationships.

    • Main Results:

    • NEMBASE provides centralized access to a large collection of parasitic nematode sequence data.
    • The database offers processed, non-redundant gene objects for efficient analysis.
    • Users can perform complex queries and comparative analyses using integrated tools.
    • The platform is actively expanding to include more species and enhanced features.

    Conclusions:

    • NEMBASE serves as a valuable resource for the scientific community studying parasitic nematodes.
    • The database facilitates ease of use and advanced analysis of nematode genetic data.
    • Future developments will further enhance its utility for nematode genomics and functional annotation.