EST2Prot: Mapping EST sequences to proteins
Open Access
- 4 March 2006
- journal article
- Published by Springer Nature in BMC Genomics
- Vol. 7 (1)
- https://doi.org/10.1186/1471-2164-7-41
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/.Keywords
This publication has 31 references indexed in Scilit:
- BIOZON: a system for unification, management and analysis of heterogeneous biological dataBMC Bioinformatics, 2006
- MRP9, an unusual truncated member of the ABC transporter superfamily, is highly expressed in breast cancerProceedings of the National Academy of Sciences, 2002
- The Protein Data Bank: unifying the archiveNucleic Acids Research, 2002
- DIANA-EST: a statistical analysisBioinformatics, 2001
- MRP8, A New Member of ABC Transporter Superfamily, Identified by EST Database Mining and Gene Prediction Program, Is Highly Expressed in Breast CancerMolecular Medicine, 2001
- The InterPro database, an integrated documentation resource for protein families, domains and functional sitesNucleic Acids Research, 2001
- BIND--The Biomolecular Interaction Network DatabaseNucleic Acids Research, 2001
- STACK: Sequence Tag Alignment and Consensus KnowledgebaseNucleic Acids Research, 2001
- The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic speciesNucleic Acids Research, 2001
- ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.1999