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

Teri Evans1, Matthew Loose2

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Summary
This summary is machine-generated.

AlignWise accurately identifies and corrects frame-shifts in protein-coding genes from species lacking reference genomes. This tool aids phylogenetic analysis of novel transcriptome and EST sequences.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying protein-coding genes in species without reference genomes is challenging due to sequencing errors like insertions and deletions.
  • Existing tools for correcting frame-shifts often fail to output DNA sequences necessary for phylogenetic analysis.
  • The Genewise algorithm, while effective, corrects frame-shifts accurately only 60% of the time and requires a homology wrapper.

Purpose of the Study:

  • To develop a novel computational tool for accurate identification and correction of frame-shifts in protein-coding genes.
  • To enable robust phylogenetic analysis of transcriptome and EST sequences from species lacking a reference genome.

Main Methods:

  • Developed AlignWise, integrating the Genewise algorithm with a novel homology-based method, AlignFS.
  • Compared the performance of AlignWise against existing open reading frame finding software.
  • Evaluated accuracy in correcting frame-shifts across varying evolutionary distances.

Main Results:

  • The AlignFS algorithm demonstrates higher accuracy than Genewise in correcting frame-shifts within an order.
  • AlignWise outperforms both AlignFS and Genewise individually, providing superior accuracy at higher evolutionary distances.
  • AlignWise successfully identifies and corrects frame-shifts with high accuracy, producing a single open reading frame (ORF) per transcript.

Conclusions:

  • AlignWise is a highly accurate tool for identifying and correcting frame-shifts in protein-coding regions.
  • The tool is well-suited for analyzing novel transcriptome assemblies and EST sequences when a reference genome is unavailable.
  • AlignWise facilitates downstream phylogenetic analyses by providing corrected DNA sequences.