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Aligning Protein-Coding Nucleotide Sequences with MACSE.

Vincent Ranwez1, Nathalie Chantret2, Frédéric Delsuc3

  • 1AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France. ranwez@supagro.fr.

Methods in Molecular Biology (Clifton, N.J.)
|December 8, 2020
PubMed
Summary
This summary is machine-generated.

Multiple Alignment of Coding Sequences (MACSE) v2 offers an updated, user-friendly solution for aligning protein-coding genes, even with frameshifts and stop codons. This tool facilitates accurate evolutionary and genomic analyses by improving codon alignment reliability.

Keywords:
Bioinformatics pipelinesMetabarcodingMolecular evolutionMultiple sequence alignmentPhylogenomicsPseudogenes

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Accurate multiple sequence alignments are crucial for genomic and evolutionary analyses.
  • Protein-coding nucleotide sequences present unique alignment challenges due to their codon structure.
  • Existing methods struggle with functional and nonfunctional sequences, including pseudogenes, frameshifts, and stop codons.

Purpose of the Study:

  • To provide a practical overview and usage guidelines for MACSE v2.
  • To highlight the advancements in MACSE v2 for aligning protein-coding sequences.
  • To introduce new pipelines for handling large datasets with MACSE v2.

Main Methods:

  • Utilizing the MACSE v2 program for multiple sequence alignment of protein-coding genes.
  • Employing unique features of MACSE to handle frameshifts and stop codons.
  • Leveraging new pipelines and Singularity containers for large-scale dataset analysis.

Main Results:

  • MACSE v2 provides reliable codon alignments in the presence of genetic anomalies like frameshifts and stop codons.
  • The updated version features a graphical interface for enhanced user-friendliness.
  • New pipelines enable efficient alignment of large protein-coding sequence datasets.

Conclusions:

  • MACSE v2 offers a robust and accessible solution for aligning protein-coding sequences, essential for evolutionary studies.
  • The software facilitates downstream analyses, such as selection pressure assessments.
  • MACSE v2 and its associated pipelines are valuable tools for the bioinformatics community.