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Novel Sequence Discovery by Subtractive Genomics
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Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly.

Dustin J Wcisel1, J Thomas Howard1, Jeffrey A Yoder1,2,3

  • 1Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA.

BMC Evolutionary Biology
|April 2, 2020
PubMed
Summary
This summary is machine-generated.

TOAST is a new R software package that helps researchers easily assemble orthologous sequences from transcriptomes for phylogenomic studies. It automates alignment generation and allows analysis of missing data, improving comparative transcriptomics.

Keywords:
BUSCO ortholog assemblyCetacean and teleost fish phylogenyConcatenated alignmentMissing data visualizationTranscriptome

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-generation sequencing has enabled extensive transcriptome analysis, generating vast public data for phylogenomics.
  • However, a lack of specialized tools hinders efficient identification of orthologous sequences from this data.

Purpose of the Study:

  • To introduce TOAST, an open-source R package designed to streamline the assembly of orthologous sequences for phylogenomic analyses.
  • To provide a solution for phylogeneticists to effectively utilize the growing volume of transcriptomic data.

Main Methods:

  • TOAST utilizes Benchmarking Universal Single-Copy Orthologs (BUSCO) for ortholog searches.
  • It automates the process of searching, querying, and assembling multiple sequence alignments of orthologous loci from transcriptomes.
  • The software generates locus and concatenated alignments, offering outputs for missing data analysis and reassembly.

Main Results:

  • TOAST automates the generation of locus and concatenated alignments from transcriptomic data.
  • It provides tools to explore missing data patterns and reassemble alignments based on user-defined thresholds.
  • The package facilitates the assembly of both public and novel sequences for any target ortholog database.

Conclusions:

  • TOAST offers a comprehensive solution for assembling orthologous sequence alignments for comparative transcriptomic and phylogenomic studies.
  • The software empowers researchers to quantify and assess the impact of missing data in their analyses.
  • As open-source software, TOAST is customizable for integration into various bioinformatic pipelines for phylogenomic inference.