Wylie, Todd and Martin, John and Abubucker, Sahar and Yin, Yong and Messina, David and Wang, Zhengyuan and McCarter, James P. and Mitreva, Makedonka (2008) NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics, 9 (525). pp. 1-10.
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Abstract
Background: Nematode.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.
Conclusion: The 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.
| Item Type: | Article |
|---|---|
| Subjects: | Medical and Health Sciences > Basic medicine |
| Divisions: | Faculty of Medical Science |
| Depositing User: | Mirjana Kocaleva Vitanova |
| Date Deposited: | 30 Nov 2012 14:31 |
| Last Modified: | 30 Nov 2012 14:31 |
| URI: | https://eprints.ugd.edu.mk/id/eprint/2623 |
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