MOTIVATION: Alternative splicing has the potential to generate a wide range of protein isoforms. For many computational applications and for experimental research, it is important to be able to concentrate on the isoform that retains the core biological function. For many genes this is far from clear. RESULTS: We have combined five methods into a pipeline that allows us to detect the principal variant for a gene. Most of the methods were based on conservation between species, at the level of both gene and protein. The five methods used were the conservation of exonic structure, the detection of non-neutral evolution, the conservation of functional residues, the existence of a known protein structure and the abundance of vertebrate orthologues. The pipeline was able to determine a principal isoform for 83% of a set of well-annotated genes with multiple variants.
MOTIVATION: Alternative splicing has the potential to generate a wide range of protein isoforms. For many computational applications and for experimental research, it is important to be able to concentrate on the isoform that retains the core biological function. For many genes this is far from clear. RESULTS: We have combined five methods into a pipeline that allows us to detect the principal variant for a gene. Most of the methods were based on conservation between species, at the level of both gene and protein. The five methods used were the conservation of exonic structure, the detection of non-neutral evolution, the conservation of functional residues, the existence of a known protein structure and the abundance of vertebrate orthologues. The pipeline was able to determine a principal isoform for 83% of a set of well-annotated genes with multiple variants.
Authors: H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971
Authors: Michael L Tress; Pier Luigi Martelli; Adam Frankish; Gabrielle A Reeves; Jan Jaap Wesselink; Corin Yeats; Páll Isólfur Olason; Mario Albrecht; Hedi Hegyi; Alejandro Giorgetti; Domenico Raimondo; Julien Lagarde; Roman A Laskowski; Gonzalo López; Michael I Sadowski; James D Watson; Piero Fariselli; Ivan Rossi; Alinda Nagy; Wang Kai; Zenia Størling; Massimiliano Orsini; Yassen Assenov; Hagen Blankenburg; Carola Huthmacher; Fidel Ramírez; Andreas Schlicker; France Denoeud; Phil Jones; Samuel Kerrien; Sandra Orchard; Stylianos E Antonarakis; Alexandre Reymond; Ewan Birney; Søren Brunak; Rita Casadio; Roderic Guigo; Jennifer Harrow; Henning Hermjakob; David T Jones; Thomas Lengauer; Christine A Orengo; László Patthy; Janet M Thornton; Anna Tramontano; Alfonso Valencia Journal: Proc Natl Acad Sci U S A Date: 2007-03-19 Impact factor: 11.205
Authors: Raghothama Chaerkady; Dhanashree S Kelkar; Babylakshmi Muthusamy; Kumaran Kandasamy; Sutopa B Dwivedi; Nandini A Sahasrabuddhe; Min-Sik Kim; Santosh Renuse; Sneha M Pinto; Rakesh Sharma; Harsh Pawar; Nirujogi Raja Sekhar; Ajeet Kumar Mohanty; Derese Getnet; Yi Yang; Jun Zhong; Aditya P Dash; Robert M MacCallum; Bernard Delanghe; Godfree Mlambo; Ashwani Kumar; T S Keshava Prasad; Mobolaji Okulate; Nirbhay Kumar; Akhilesh Pandey Journal: Genome Res Date: 2011-07-27 Impact factor: 9.043
Authors: Iakes Ezkurdia; Angela del Pozo; Adam Frankish; Jose Manuel Rodriguez; Jennifer Harrow; Keith Ashman; Alfonso Valencia; Michael L Tress Journal: Mol Biol Evol Date: 2012-03-22 Impact factor: 16.240
Authors: Jennifer Harrow; Adam Frankish; Jose M Gonzalez; Electra Tapanari; Mark Diekhans; Felix Kokocinski; Bronwen L Aken; Daniel Barrell; Amonida Zadissa; Stephen Searle; If Barnes; Alexandra Bignell; Veronika Boychenko; Toby Hunt; Mike Kay; Gaurab Mukherjee; Jeena Rajan; Gloria Despacio-Reyes; Gary Saunders; Charles Steward; Rachel Harte; Michael Lin; Cédric Howald; Andrea Tanzer; Thomas Derrien; Jacqueline Chrast; Nathalie Walters; Suganthi Balasubramanian; Baikang Pei; Michael Tress; Jose Manuel Rodriguez; Iakes Ezkurdia; Jeltje van Baren; Michael Brent; David Haussler; Manolis Kellis; Alfonso Valencia; Alexandre Reymond; Mark Gerstein; Roderic Guigó; Tim J Hubbard Journal: Genome Res Date: 2012-09 Impact factor: 9.043
Authors: Jose Manuel Rodriguez; Paolo Maietta; Iakes Ezkurdia; Alessandro Pietrelli; Jan-Jaap Wesselink; Gonzalo Lopez; Alfonso Valencia; Michael L Tress Journal: Nucleic Acids Res Date: 2012-11-17 Impact factor: 16.971
Authors: Gonzalo Lopez; Paolo Maietta; Jose Manuel Rodriguez; Alfonso Valencia; Michael L Tress Journal: Nucleic Acids Res Date: 2011-06-14 Impact factor: 16.971
Authors: Recep Colak; TaeHyung Kim; Magali Michaut; Mark Sun; Manuel Irimia; Jeremy Bellay; Chad L Myers; Benjamin J Blencowe; Philip M Kim Journal: PLoS Comput Biol Date: 2013-04-25 Impact factor: 4.475