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EST2Prot: mapping EST sequences to proteins.

Paul Shafer·David M Lin·Golan Yona
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Abstract

BACKGROUND: EST libraries are used in various biological studies, from microarray experiments to proteomic and genetic screens. These libraries usually contain many uncharacterized ESTs that are typically ignored since they cannot be mapped to known genes. Consequently, new discoveries are possibly overlooked. RESULTS: We describe a system (EST2Prot) that uses multiple elements to map EST sequences to their corresponding protein products. EST2Prot uses UniGene clusters, substring analysis, information about protein coding regions in existing DNA sequences and protein database searches to detect protein products related to a query EST sequence. Gene Ontology terms, Swiss-Prot keywords, and protein similarity data are used to map the ESTs to functional descriptors. CONCLUSION: EST2Prot extends and significantly enriches the popular UniGene mapping by utilizing multiple relations between known biological entities. It produces a mapping between ESTs and proteins in real-time through a simple web-interface. The system is part of the Biozon database and is accessible at http://biozon.org/tools/est/.

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AnimalsChromosome MappingComputational BiologyDatabase Management SystemsDatabases, ProteinExpressed Sequence TagsHumansProteinsSequence Analysis, DNAUser-Computer InterfaceJournal ArticleResearch Support, U.S. Gov't, Non-P.H.S.

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Paul Shafer, David M Lin, Golan Yona. 2006-03-04. EST2Prot: mapping EST sequences to proteins.. https://doi.org/10.1186/1471-2164-7-41

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