title: 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, 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.
  
  
  CONCLUSIONS
  AlignWise 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.
authors.affiliation: School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK. teri.evans@nottingham.ac.uk.
authors.forename: Teri
authors.initials: T
authors.lastname: Evans
authors.affiliation: School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK. matt.loose@nottingham.ac.uk.
authors.forename: Matthew
authors.initials: M
authors.lastname: Loose
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D016368:Frameshift Mutation / Q000235:genetics*; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D012984:Software