A dotplot program for the Atari ST, for the analysis of DNA and protein sequences

Area of Science:

• Bioinformatics
• Computational Biology
• Molecular Biology

Background:

• Homology detection is crucial for understanding protein and DNA sequence relationships.
• Visualizing sequence similarity aids in identifying functional and evolutionary patterns.
• Existing tools may lack user-friendliness or speed for certain platforms.

Purpose of the Study:

• To develop a user-friendly program for generating 2D homology dotplots.
• To enable rapid comparison of protein and DNA sequences.
• To leverage the Atari ST microcomputer for bioinformatics tasks.

Main Methods:

• Implementation of a GFA-BASIC program on the Atari ST microcomputer.
• Integration of a machine-code subroutine for enhanced performance.
• Development of an interactive user interface with dialogue panels and mouse input.

Main Results:

• Successful generation of two-dimensional homology dotplots for sequence comparison.
• Interactive user communication and mouse-directed input facilitate ease of use.
• Achieved a sequence comparison speed of 12 seconds for a 1000x1000 comparison with specific stringency.

Conclusions:

• The developed program provides an efficient and accessible method for homology dotplot generation.
• The program demonstrates the utility of microcomputers for specific bioinformatics applications.
• Interactive design enhances user experience in sequence analysis.