Dataset Information

Determination and validation of principal gene products.

ABSTRACT: 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.

SUBMITTER: Tress ML

PROVIDER: S-EPMC2734078 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature

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Determination and validation of principal gene products.

Tress Michael L ML Wesselink Jan-Jaap JJ Frankish Adam A López Gonzalo G Goldman Nick N Löytynoja Ari A Massingham Tim T Pardi Fabio F Whelan Simon S Harrow Jennifer J Valencia Alfonso A

Bioinformatics (Oxford, England) 20071115 1

<h4>Motivation</h4>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.<h4>Results</h4>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 ...[more]

PMID: 18006548

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Dataset Information

Determination and validation of principal gene products.

Publications

Determination and validation of principal gene products.

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