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

ABSTRACT:

Background

Identifying 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.

Results

We 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,

SUBMITTER: Evans T 

PROVIDER: S-EPMC4640205 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature