Nematode.net explained

Nematode.net is a publicly available resource dedicated to the study of parasitic nematodes.^{[1] [2]} It stemmed from an Expressed Sequence Tag (EST) project that began at The Genome Institute at Washington University School of Medicine. The site was launched in 2000 to accompany the project “A Genomic Approach to Parasites from the Phylum Nematoda,”^[3] funded by the National Institute of Allergy and Infectious Diseases (NIAID). It was created to provide access to the data from this project and as a broader resource for the scientific community studying parasitic nematodes.^[4]

History

The first model nematode to be sequenced was Caenorhabditis elegans. It was also the first fully sequenced genome of a multicellular organism to be completed.^[5] Nematode.net built on these efforts to make available the gene sequences from medically and economically relevant parasitic nematodes. Human parasitic nematodes, or roundworms, have wide-ranging global health implications, producing a disease burden that exceeds malaria and tuberculosis.^[6] Plant parasitic nematodes cause over $100 billion in annual crop damage worldwide.^[7]

Tools

When Nematode.net began in 2000, it provided a searchable repository for nematode EST sequences that were not available elsewhere. The site now also provides tools for viewing protein and metabolic pathways,^[8] and a comparative genomics platform that can aid in nematode drug, vaccine and pesticide research.^[9]

Tools available on Nematode.net include:

• HelmCoP - an online resource aiming to help researchers develop strategies for drug, vaccine and pesticide prioritization, while also providing a useful comparative genomics platform.^[10]
• NemaBLAST - a tool allowing the alignment of user defined protein or nucleotide sequence against nematode transcripts or cDNA reads organized by organism or library.^[11]
• NemaPath - a tool for exploring metabolic (and other) pathways in various nematodes. In single organism mode this tool populates pathway images by merit of aligning transcripts or genes to KEGG Orthology (KO) ids that are known to exist in that pathway. In dual organism mode this tool allows for the comparison of the pathway usage of any two nematodes in the database. Host and clade specific comparative views are also available.^[12]
• NemaGene - a data mining tool allowing the user to search for transcripts by name, or to explore transcript expression by life cycle stage in a given organism.^[13]
• NemaFam - a collection of nematode-related conserved regions of proteins.^[14]
• NemaBrowse - a data viewer for genes predicted from nematode genomes.^[15]
• NemaSNP - an online resource showing genetic variations among populations of nematodes.^[16]

Notes and References

1. Martin J, Abubucker S, Heizer E, Taylor CM, Mitreva M. (2012) Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. "Nucleic Acids Research." 40 (Database issue): D720-D728.
2. Martin J, Abubucker S, Wylie T, Yin Y, Wang Z, Mitreva M. (2009) Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. Nucleic Acids Research. 37 (suppl 1): D571-D578.
3. NIH Project Information on "'A Genomic Approach to Parasites from the Phylum Nematoda’"
4. Wylie T, Martin J, Dante M, Mitreva M, Clifton SC, Chinwalla A, Waterston RH, Wilson RK, McCarter JP. (2004) Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes Nucleic Acids Research. 32 (suppl 1): D423-D426.
5. C. elegans Sequencing Consortium. (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. Dec 11;282(5396): 2012-8.
6. Hotez PJ, Brindley PJ, Bethony JM, King CH, Pearce EJ, Jacobson J. (2008) Helminth infections: the great neglected tropical diseases. Journal of Clinical Investigation. Apr;118(4):1311-21.
7. Jasmer DP, Groverse A, Smant, G. (2003) Parasitic nematode interactions with mammals and plants. Annu. Rev. Phytopathol. 41, 245–270.
8. Wylie T, Martin J, Abubucker S, Yin Y, Messina D, Wang Z, McCarter JP, Mitreva M. (2009) NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics. 4;9:525.
9. Abubucker S, Martin J, Taylor CM, Mitreva M. (2011) HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization. PLoS One. 6(7):e21832. Epub 2011 Jul 8.
10. Web site: HelmCoP. nematode.net.
11. Web site: NemaBLAST . nematode.net.
12. Web site: NemaPath. nematode.net.
13. Web site: NemaGene. nematode.net.
14. Web site: NemaFam. nematode.net.
15. Web site: NemaBrowser. nematode.net.
16. Web site: NemaSNP. nematode.net.