Nematode.net

Nematode.net provides a public bioinformatics platform for nematode research, integrating organism-specific portals for over 56 species, sequence alignment and browsing (NemaBLAST, NemaBrowse), KEGG Orthology (KO)-based metabolic pathway reconstruction (NemaPath), SNP analysis from next-generation sequencing (NemaSNP), and comparative genomics and genome annotation resources (HelmCoP) to support functional and comparative studies.

Key Features:

• Organism-Centric Portals: Dynamically generated portals for over 56 nematode species offering species-specific datasets and analysis access.
• NemaBLAST: Sequence alignment searches against an extensive nematode sequence database.
• NemaBrowse: Genomic data browsing that provides views of gene structure and genome organization across nematodes.
• NemaPath (Metabolic Pathway Analysis): Metabolic pathway construction using KEGG Orthology (KO) identifiers instead of Enzyme Commission (EC) numbers to describe protein functions.
• NemaSNP: Analysis of single nucleotide polymorphisms (SNPs) from next-generation sequencing data for population genetics studies.
• HelmCoP (Helminth Control and Prevention): Storage, annotation, and comparative genomics of helminth genomes to support identification of candidate drug, pesticide, and vaccine targets.

Scientific Applications:

• Comparative Genomics: Identification of evolutionary relationships among nematodes using genome-scale comparisons.
• Population Genetics: Analysis of genetic diversity and adaptation in nematode populations via SNP data from NGS.
• Metabolic Pathway Analysis: Elucidation of nematode metabolic pathways and protein functions using KO-based pathway models.
• Target Discovery for Control Measures: Annotation-driven discovery of potential drug, pesticide, and vaccine targets using HelmCoP comparative analyses.
• Genome Annotation and Storage: Aggregation and annotation of helminth genomic datasets for downstream analysis.

Methodology:

Sequence alignment via NemaBLAST; genomic browsing via NemaBrowse; metabolic pathway construction using KEGG Orthology (KO) identifiers in NemaPath; SNP analysis of next-generation sequencing data in NemaSNP; storage, annotation, and comparative genomics through HelmCoP; dynamically generated organism-specific portals.