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Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics.
John Martin1, Sahar Abubucker, Todd Wylie
1The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA.
Nucleic Acids Research
|October 23, 2008
Summary
Nematode.net provides a centralized resource for parasitic nematode research, offering extensive expressed sequence tags (ESTs) and genomic data for gene discovery. This platform facilitates access to assembled gene clusters, functional annotations, and conserved protein families for the scientific community.
Area of Science:
- Parasitology
- Genomics
- Bioinformatics
Background:
- Parasitic nematodes pose significant threats to human, animal, and plant health.
- Gene discovery in these organisms is crucial for developing control strategies.
- Existing resources for parasitic nematode genomics were fragmented and limited.
Purpose of the Study:
- To establish a comprehensive, publicly accessible database for parasitic nematode genomic and expressed sequence data.
- To facilitate gene discovery and functional analysis in non-Caenorhabditis elegans nematodes.
- To provide a centralized and enduring platform for disseminating research findings.
Main Methods:
- Generation of over 500,000 expressed sequence tags (ESTs) and 1.2 million genome survey sequences.
- Assembly of sequences into NemaGene clusters.
- Integration of functional annotations (Gene Ontology, KEGG pathways) and protein family analysis (NemFam).
Main Results:
- Nematode.net was developed, offering user-friendly access to a vast collection of ESTs and genomic data from over 30 nematode species.
- The resource includes assembled gene clusters, functional annotations, metabolic pathway mapping, codon usage tables, and conserved protein families.
- A web-based WU-BLAST tool enables complex data querying.
Conclusions:
- Nematode.net serves as a vital, centralized hub for parasitic nematode research.
- The platform significantly enhances gene discovery and functional characterization in parasitic nematodes.
- It provides a robust and enduring resource for the global scientific community.
