Multiple genome sequences alignment algorithm based on coding regions.

Area of Science:

• Computational Biology
• Bioinformatics
• Genomics

Background:

• Multiple Sequence Alignment (MSA) is crucial for DNA homology, phylogeny, and motif studies.
• Existing MSA tools effectively align protein, DNA, and RNA but struggle with coding regions.

Purpose of the Study:

• To introduce CORAL-M, a novel heuristic alignment method specifically designed for multiple genome sequences, with a focus on coding regions.
• To address the limitations of current MSA tools in aligning coding sequences.

Main Methods:

• CORAL-M utilizes a codon-based probabilistic filtration model.
• It employs a local optimal alignment solution for efficient processing.
• The method achieves linear time complexity for alignment.

Main Results:

• CORAL-M demonstrated superior performance in aligning Enterovirus strains.
• The tool identified a greater number of potential functional sites compared to commonly used MSA methods.
• Experimental results validate the effectiveness of the codon-based approach.

Conclusions:

• CORAL-M offers an effective solution for multiple genome sequence alignment, particularly for coding regions.
• The method enhances the discovery of functional sites in genomic data.
• CORAL-M represents a significant advancement in computational biology tools for sequence analysis.