MALIGNED: a multiple sequence alignment editor

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Multiple sequence alignment is crucial for understanding evolutionary relationships and functional similarities between biological sequences.
• Existing alignment editors may lack advanced visualization or data exchange capabilities.
• The Genetics Computer Group (GCG) provides a suite of tools widely used in bioinformatics.

Purpose of the Study:

• To describe a novel multiple sequence alignment editor designed for the VAX/VMS operating system.
• To enable seamless data exchange with other bioinformatics software, including GCG.
• To provide enhanced tools for assessing and visualizing sequence alignment quality.

Main Methods:

• The editor runs on a VAX/VMS system.
• It supports data exchange with external programs, specifically mentioning GCG.
• Alignment quality is visualized through character display attributes based on sequence matching.
• Four distinct methods for calculating highlighting and up to four highlighting styles can be employed simultaneously.

Main Results:

• The editor can align up to 199 sequences.
• Users can easily assess alignment quality during development via character highlighting.
• Multiple highlighting methods and styles allow for detailed visualization of sequence relationships.
• The system generates laser printer output suitable for direct publication.

Conclusions:

• The developed multiple sequence alignment editor offers a powerful and versatile tool for bioinformatics research.
• Its integration capabilities and advanced visualization features facilitate efficient sequence analysis and interpretation.
• The editor produces publication-quality output, streamlining the process of scientific communication.