AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts

BMC Bioinformatics

Software

Matthew Loose¹  Teri Evans¹ 

[1]School of Life Sciences, University of Nottingham, NG7 2UH, Nottingham, UK

关键词: Frame-shift;    Protein-coding;    Homology;    Open reading frame;    Genewise;   

DOI  :  10.1186/s12859-015-0813-8

 received in 2015-07-24, accepted in 2015-10-31,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundIdentifying protein-coding genes from species without a reference genome sequence can be complicated by the presence of sequencing errors, particularly insertions and deletions. A number of tools capable of correcting erroneous frame-shifts within assembled transcripts are available but often do not report back DNA sequences required for subsequent phylogenetic analysis. Amongst those that do, the Genewise algorithm is the most effective. However, it requires a homology wrapper to be used in this way, and here we demonstrate it perfectly corrects frame-shifts only 60 % of the time.ResultsWe therefore created AlignWise, a tool that combines Genewise with our own homology-based method, AlignFS, to identify protein-coding regions and correct erroneous frame-shifts, suitable for subsequent phylogenetic analysis. We compared AlignWise against other open reading frame finding software and demonstrate that the AlignFS algorithm is more accurate than Genewise at correcting frame-shifts within an order. We show that AlignWise provides the greatest accuracy at higher evolutionary distances, out-performing both AlignFS and Genewise individually.ConclusionsAlignWise produces a single ORF per transcript and identifies and corrects frame-shifts with high accuracy. It is therefore well suited for analysing novel transcriptome assemblies and EST sequences in the absence of a reference genome.

【 授权许可】

CC BY   
© Evans and Loose. 2015