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MALIGNED: a multiple sequence alignment editor.

S P Clark1

  • 1Division of Cellular and Molecular Biology, Ontario Cancer Institute, Toronto, Canada.

Computer Applications in the Biosciences : CABIOS
|December 1, 1992
PubMed
Summary
This summary is machine-generated.

This study introduces a multiple sequence alignment editor for VAX/VMS systems, facilitating data exchange with programs like GCG. It enhances alignment quality assessment through character display attributes and multiple highlighting options for publication-ready output.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Effective visualization is crucial for analyzing multiple sequence alignments.
  • Existing tools may lack integrated features for quality assessment and data exchange.

Purpose of the Study:

  • To describe a novel multiple sequence alignment editor for VAX/VMS systems.
  • To enhance the process of developing and evaluating sequence alignments.
  • To provide publication-ready output directly from the editor.

Main Methods:

  • The editor runs on a VAX/VMS operating system.
  • It supports data exchange with external programs, including the Genetics Computer Group (GCG) suite.
  • Alignment quality is assessed via display attributes reflecting character matches.
  • Four distinct methods and four highlighting styles are available for visualizing sequence relationships.

Main Results:

  • The system can align up to 199 sequences simultaneously.
  • Character display attributes dynamically reflect alignment quality.
  • Multiple highlighting methods and styles can be combined for detailed analysis.
  • Laser printer output is directly suitable for scientific publications.

Conclusions:

  • The developed multiple sequence alignment editor offers a powerful and integrated solution for sequence analysis.
  • Its features facilitate easier quality judgment and visualization of sequence relationships.
  • The system streamlines the workflow from alignment development to publication.