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Abstract
BackgroundNematode.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.DescriptionHere 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 . The nematode source sequences used for the metabolic pathway mappings are available via FTP , as provided by the Genome Center at Washington University School of Medicine.
Highlights
Nematode.net http://www.nematode.net is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes
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
Example, a pan-phylum analysis based on 93,000 genes of partial genomes in 32 nematode species when compared to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database identified taxonomically restricted biochemical pathways that may serve to direct drug target definition [32]
Summary
NemaPath, the database described provides the research community a unique resource for pathway visualization of multi-species nematode genomic data in terms of KEGG database vocabulary. NemaPath is part of the larger Nematode.net web resource and integrates well with the site's previous functionality, streamlining access to significant internal nematode sequence data, as well as http://www.biomedcentral.com/1471-2164/9/525 information provided by off-site resources at NEMBASE3 [40] and WormBase [41] repositories. Plaintext file versions of alignment information (as compiled by KEGGscan) are available by species http://www.nem atode.net/FTP/nemapath_ftp/index.php. The most current NemaGene EST cluster builds are available via FTP at http://nematode.net/FTP/cluster_ftp/index.php after completing a short access form. JM, SA, and DM helped develop software and informatics approaches for the Nematode.net web site. All authors contributed to the writing and editing of this manuscript
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