ArticleBMC genomics2008
NemaPath: online exploration of KEGG-based metabolic pathways for nematodes.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
17 citing papers in PubMed.
- De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells.PLoS neglected tropical diseases · 2020Article
- Analysis of the Trichuris suis excretory/secretory proteins as a function of life cycle stage and their immunomodulatory properties.Scientific reports · 2018Article
- A Multi-Omics Database for Parasitic Nematodes and Trematodes.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini.Parasites & vectors · 2016Article
- The glyoxylate shunt is essential for desiccation tolerance in C. elegans and budding yeast.eLife · 2016Article
- Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2016Article
- An Integrated Multiomics Approach to Identify Candidate Antigens for Serodiagnosis of Human Onchocerciasis.Molecular & cellular proteomics : MCP · 2015Article
- Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock.Biotechnology advances · 2015Review
- Pan-phylum Comparison of Nematode Metabolic Potential.PLoS neglected tropical diseases · 2015Article
- Helminth.net: expansions to Nematode.net and an introduction to Trematode.net.Nucleic acids research · 2015Article
- Systems biology studies of adult paragonimus lung flukes facilitate the identification of immunodominant parasite antigens.PLoS neglected tropical diseases · 2014Article
- Profiling the anaerobic response of C. elegans using GC-MS.PloS one · 2012Article
- A research agenda for helminth diseases of humans: basic research and enabling technologies to support control and elimination of helminthiases.PLoS neglected tropical diseases · 2012Review
- Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data.Nucleic acids research · 2012Article
- Global expression analysis revealed novel gender-specific gene expression features in the blood fluke parasite Schistosoma japonicum.PloS one · 2011Article
- The draft genome of the parasitic nematode Trichinella spiralis.Nature genetics · 2011Article
- A metabolic signature of long life in Caenorhabditis elegans.BMC biology · 2010Article
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Authors and funding
8 authors.
Funding
Abstract
backgroundNematode.net http://www.nematode.net is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes. Beyond the well-characterized model nematode C. elegans, over 500,000 expressed sequence tags (ESTs) and nearly 600,000 genome survey sequences (GSSs) have been generated from 36 nematode species as part of the Parasitic Nematode Genomics Program undertaken by the Genome Center at Washington University School of Medicine. However, these sequencing data are not present in most publicly available protein databases, which only include sequences in Swiss-Prot. Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for predicted proteins from complete genomes or full-length proteins. DESCRIPTION: Here we present the NemaPath pathway server, a web-based pathway-level visualization tool for navigating putative metabolic pathways for over 30 nematode species, including 27 parasites. The NemaPath approach consists of two parts: 1) a backend tool to align and evaluate nematode genomic sequences (curated EST contigs) against the annotated Kyoto Encyclopedia of Genes and Genomes (KEGG) protein database; 2) a web viewing application that displays annotated KEGG pathway maps based on desired confidence levels of primary sequence similarity as defined by a user. NemaPath also provides cross-referenced access to nematode genome information provided by other tools available on Nematode.net, including: detailed NemaGene EST cluster information; putative translations; GBrowse EST cluster views; links from nematode data to external databases for corresponding synonymous C. elegans counterparts, subject matches in KEGG's gene database, and also KEGG Ontology (KO) identification.
conclusionThe NemaPath server hosts metabolic pathway mappings for 30 nematode species and is available on the World Wide Web at http://nematode.net/cgi-bin/keggview.cgi. The nematode source sequences used for the metabolic pathway mappings are available via FTP http://www.nematode.net/FTP/index.php, as provided by the Genome Center at Washington University School of Medicine.
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