transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Multiple sequence alignment is critical for comparative genomics and phylogenetic analysis.
• Aligning protein-coding DNA via amino acid sequences offers speed and accuracy advantages.
• Existing translated alignment tools are often incomplete, hindering large-scale automated applications.

Purpose of the Study:

• To develop a comprehensive and automated solution for aligning protein-coding DNA sequences using translated alignments.
• To improve the efficiency and accuracy of DNA sequence alignment for large datasets.

Main Methods:

• The transAlign script translates DNA sequences into amino acids.
• It utilizes ClustalW for amino acid sequence alignment.
• The aligned amino acid sequences are then back-translated to produce aligned DNA sequences, with options for handling frame shifts.

Main Results:

• transAlign provides a full, cross-platform implementation of translated alignments.
• The method demonstrably improves alignment speed and accuracy for protein-coding DNA sequences.
• Benchmarks show consistent performance gains across various datasets.

Conclusions:

• transAlign is highly suitable for large-scale, automated alignment of numerous protein-coding DNA datasets.
• The program offers user-definable options and robust performance.
• It is freely available as open-source software.