Electronic Thesis/Dissertation


SNVDis: A protein-centric non-synonymous variation analysis service for genome-wide analysis of active sites, binding sites, pathways and protein domains. Open Access

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Amino acid changes due to non-synonymous variation are included as annotations for individual proteins in UniProtKB/Swiss-Prot, RefSeq and other databases which present biological data in a protein- or gene-centric fashion. Unfortunately, proteome-wide analysis of nsSNVs is not easy to perform because information on nsSNVs and functionally important sites are not well integrated both within and between databases and their search engines. We have collected data from major variation databases (UniProtKB, dbSNP, neXtProt and COSMIC) and comprehensive sequence feature annotation from UniProtKB, Pfam, RefSeq, Conserved domain database (CDD) and pathway information from Panther and mapped all of them in a uniform and comprehensive way to the human reference proteome provided by UniProtKB/Swiss-Prot. Integrated information of active sites, pathways, binding sites, domains, pathways, which are extracted from a number of different sources, give a detailed overview of how nsSNVs are distributed over the human proteome and pathways and how they intersect with functional sites of proteins. Additionally, it is possible to find out if there is an over- or under-representation of nsSNVs in specific domains, pathways, user-defined protein lists, or user-defined sets of protein ranges. The underlying datasets are updated once every two months.Availability:  http://hive.biochemistry.gwu.edu/usr/karagiak/snpdis.cgi?cmd=snpdis

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