Apr 10, 2020

Choosing representative proteins based on splicing structure similarity improves the accuracy of gene tree reconstruction

BioRxiv : the Preprint Server for Biology
Esaie Kuitche KamelaAida Ouangraoua

Abstract

Constructing accurate gene trees is important, as gene trees play a key role in several biological studies, such as species tree reconstruction, gene functional analysis and gene family evolution studies. The accuracy of these studies is dependent on the accuracy of the input gene trees. Although several methods have been developed for improving the construction and the correction of gene trees by making use of the relationship with a species tree in addition to multiple sequence alignment, there is still a large room for improvement on the accuracy of gene trees and the computing time. In particular, accounting for alternative splicing that allows eukaryote genes to produce multiple transcripts/proteins per gene is a way to improve the quality of multiple sequence alignments used by gene tree reconstruction methods. Current methods for gene tree reconstruction usually make use of a set of transcripts composed of one representative transcript per gene, to generate multiple sequence alignments which are then used to estimate gene trees. Thus, the accuracy of the estimated gene tree depends on the choice of the representative transcripts. In this work, we present an alternative-splicing-aware method called Splicing Homology Trans...Continue Reading

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Mentioned in this Paper

Toxic Shock Syndrome
Prokaryotic potassium channel
Genome
Primary RNA Transcript
Transcription Initiation Site
Transcription, Genetic
Ribosomal RNA
Profile (Lab Procedure)
Gene Expression
Site

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