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SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies.

Wend Yam D D Ouedraogo1, Aida Ouangraoua2

  • 1Department of Computer Science, Université de Sherbrooke, 2500 Bd de l'université, Sherbrooke, QC, J1K2R1, Canada. wend.yam.donald.davy.ouedraogo@usherbrooke.ca.

BMC Bioinformatics
|July 11, 2024
PubMed
Summary
This summary is machine-generated.

SimSpliceEvol2 enhances eukaryotic gene sequence simulation by modeling transcript evolution along gene trees. This new version enables robust evaluation of transcript and gene phylogeny inference methods, improving spliced RNA sequence analysis.

Keywords:
Alternative splicingEvolutionExon-intron structureSimulationTranscript phylogeny

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Genomics

Background:

  • SimSpliceEvol simulates eukaryotic gene and transcript evolution but lacks evolutionary connections between transcripts.
  • This limitation hinders its use in evaluating transcript or gene phylogeny inference methods reliant on transcript conservation.

Purpose of the Study:

  • Introduce SimSpliceEvol2, an improved tool for simulating gene and transcript evolution.
  • Incorporate an explicit model of transcript evolution along gene trees.
  • Provide a user-friendly interface and web server for accessibility.

Main Methods:

  • Developed SimSpliceEvol2 with an explicit model for alternative transcript evolution.
  • Integrated transcript phylogeny inference into the simulation process.
  • Created a graphical user interface and updated web server for the tool.

Main Results:

  • SimSpliceEvol2 simulates transcript evolution along guide gene trees, inferring transcript phylogenies.
  • The tool generates synthetic datasets for evaluating spliced RNA sequence analysis methods.
  • A user-friendly graphical interface and web server are available.

Conclusions:

  • SimSpliceEvol2 provides valuable synthetic datasets for assessing spliced alignment, conserved transcript identification, and transcript phylogeny reconstruction methods.
  • The tool and its source code are accessible via a web server and GitHub repository.
  • Facilitates advancement in spliced RNA sequence analysis and evolutionary studies.