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RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences.

Rasmus Wernersson1, Anders Gorm Pedersen

  • 1Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, DK-2800, Lyngby, Denmark.

Nucleic Acids Research
|June 26, 2003
PubMed
Summary

Aligning DNA at the amino acid level preserves phylogenetic signal better than DNA-only alignments. The RevTrans program facilitates this by translating DNA, aligning proteins, and reverse-translating to create superior DNA alignments for evolutionary studies.

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Area of Science:

  • Bioinformatics
  • Molecular Evolution
  • Computational Biology

Background:

  • Protein sequences offer a higher signal-to-noise ratio for alignment compared to DNA due to the 20 amino acid alphabet versus DNA's 4 bases.
  • Protein alignments benefit from substitution matrices (e.g., BLOSUM-62) and retain phylogenetic signal longer than DNA sequences, which are affected by higher rates of synonymous mutations.

Purpose of the Study:

  • To develop a computational tool, RevTrans, for aligning coding DNA sequences at the amino acid level.
  • To improve the accuracy and reliability of multiple DNA alignments for phylogenetic analysis.

Main Methods:

  • RevTrans translates DNA sequences into amino acid sequences.
  • It then aligns these peptide sequences using established methods.
  • Finally, it performs 'reverse translation' to generate a multiple DNA alignment based on the protein alignment.

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Main Results:

  • The resulting DNA alignments maintain codon structure, with gaps appearing in triplets.
  • Analogous codon positions are consistently aligned, preserving evolutionary information.
  • RevTrans ensures that phylogenetic signal is retained more effectively in the DNA alignment.

Conclusions:

  • Aligning coding DNA at the amino acid level is preferable for phylogenetic analysis due to better signal retention.
  • RevTrans provides a robust method for generating high-quality multiple DNA alignments.
  • The RevTrans web server is available for researchers to utilize this alignment strategy.