EST2Prot: mapping EST sequences to proteins

BMC Genomics
Paul ShaferGolan Yona

Abstract

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. 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. 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/.

References

Jan 1, 1996·Nucleic Acids Research·D G GeorgeA Tsugita
Jan 1, 1996·Methods in Enzymology·D G GeorgeW C Barker
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 31, 1997·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·G D Schuler
Feb 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·G VasmatzisI Pastan
Dec 10, 1998·Nucleic Acids Research·H OgataM Kanehisa
Jan 11, 2000·Nucleic Acids Research·A ChristoffelsW Hide
Jan 11, 2000·Nucleic Acids Research·G D BaderC W Hogue
Oct 24, 2001·Bioinformatics·A G HatzigeorgiouM Reczko
Dec 26, 2001·Nucleic Acids Research·John WestbrookHelen M Berman
May 16, 2002·Proceedings of the National Academy of Sciences of the United States of America·Tapan K BeraIra Pastan
Oct 5, 2002·Nucleic Acids Research·Catherine MathéPierre Rouzé
Nov 1, 2002·Nucleic Acids Research·Patricia AyoubiRolf A Prade
Nov 29, 2002·Frontiers in Bioscience : a Journal and Virtual Library·Shinji HiranoChristoph Redies
Jun 26, 2003·Nucleic Acids Research·Agnes Hotz-WagenblattSándor Suhai
Oct 7, 2003·Annual Review of Genomics and Human Genetics·Jennifer L Ashurst, John E Collins
Feb 7, 2004·Bioinformatics·Werner G Krebs, Philip E Bourne
Feb 28, 2004·Bioinformatics·John ParkinsonMark Blaxter
Mar 3, 2004·Nucleic Acids Research·Eric W KleeLynda B M Ellis
Nov 6, 2004·BMC Bioinformatics·Charu G KumarLei Liu
Dec 2, 2004·BMC Bioinformatics·James D Wasmuth, Mark L Blaxter
Dec 21, 2004·Nucleic Acids Research·Amos BairochLai-Su L Yeh
Dec 31, 2005·Nucleic Acids Research·Aaron Birkland, Golan Yona
Feb 17, 2006·BMC Bioinformatics·Aaron Birkland, Golan Yona

❮ Previous
Next ❯

Citations

Aug 7, 2012·Molecular & Cellular Proteomics : MCP·Manfred Claassen
Dec 26, 2006·Pharmacogenomics·Michail Ignatiadis, Christine Desmedt

❮ Previous
Next ❯

Software Mentioned

Mozzila
BLASTX
ESTScan
BLAST
PartiGene
DECODER
EST2Prot
UniGene
PipeOnline
ESTIMA

Related Concepts

Related Feeds

Axon Guidance

Axon guidance is a complex neural developmental field that investigates mechanisms through which neurons send out axons to reach its target. Here is the latest research in this domain.

Adhesion Molecules in Health and Disease

Cell adhesion molecules are a subset of cell adhesion proteins located on the cell surface involved in binding with other cells or with the extracellular matrix in the process called cell adhesion. In essence, cell adhesion molecules help cells stick to each other and to their surroundings. Cell adhesion is a crucial component in maintaining tissue structure and function. Discover the latest research on adhesion molecule and their role in health and disease here.

Cadherins and Catenins

Cadherins (named for "calcium-dependent adhesion") are a type of cell adhesion molecule (CAM) that is important in the formation of adherens junctions to bind cells with each other. Catenins are a family of proteins found in complexes with cadherin cell adhesion molecules of animal cells: alpha-catenin can bind to β-catenin and can also bind actin. β-catenin binds the cytoplasmic domain of some cadherins. Discover the latest research on cadherins and catenins here.

Adherens Junctions

An adherens junction is defined as a cell junction whose cytoplasmic face is linked to the actin cytoskeleton. They can appear as bands encircling the cell (zonula adherens) or as spots of attachment to the extracellular matrix (adhesion plaques). Adherens junctions uniquely disassemble in uterine epithelial cells to allow the blastocyst to penetrate between epithelial cells. Discover the latest research on adherens junctions here.

Related Papers

Molecular & Cellular Proteomics : MCP
Ville R KoskinenJohn S Cottrell
Cancer Immunology, Immunotherapy : CII
Federica Cavallo, Constantin N Baxevanis
Molecular & Cellular Proteomics : MCP
Manfred ClaassenRuedi Aebersold
© 2021 Meta ULC. All rights reserved