Comparison of DNA sequences with protein sequences

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• The FASTA package is a suite of sequence comparison programs.
• Efficient comparison of DNA and protein sequences is crucial for genomic analysis.

Purpose of the Study:

• To introduce and evaluate new tools, FASTX and FASTY, within the FASTA package.
• To assess the performance and accuracy of these new tools for DNA-to-protein and protein-to-DNA sequence comparisons.

Main Methods:

• FASTX and FASTY translate DNA sequences in multiple frames for comparison against protein databases.
• TFASTX and TFASTY translate DNA databases in six frames for comparison against protein sequences.
• Performance was evaluated using varying gap penalties, frameshift, and nucleotide substitution parameters.
• Statistical estimates from FASTX and FASTY were analyzed for accuracy.

Main Results:

• FASTX and FASTY demonstrate equivalent performance with up to 10% sequence errors.
• Statistical estimates are generally accurate, with exceptions for low-complexity translated sequences.
• Application of FASTX to genomic datasets identified new protein-coding genes and corrected gene boundaries.

Conclusions:

• FASTX and FASTY are effective tools for DNA-to-protein sequence comparison.
• These tools enhance the capabilities of the FASTA package for genomic analysis and gene discovery.
• The study successfully identified novel genes and refined gene annotations in multiple microbial genomes.