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A consensus program for molecular sequences

W H Day¹, F R McMorris

¹Department of Computer Science, Memorial University of Newfoundland, St John's, Canada.

Computer Applications in the Biosciences : CABIOS

|December 1, 1993

Summary

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Molecular biologists can now analyze consensus sequence methods with the new CONSENSUS program. This tool aids in understanding and selecting appropriate methods for DNA and protein sequence analysis.

Area of Science:

Bioinformatics
Computational Biology
Molecular Biology

Background:

Consensus sequences are frequently calculated by molecular biologists from aligned DNA or protein sequences.
The properties of many consensus calculation methods remain poorly understood.

Purpose of the Study:

To develop and present a program, CONSENSUS, for analyzing and comparing various methods of calculating consensus sequences.
To provide a tool for understanding the behavior of different consensus algorithms.

Main Methods:

Developed a software program named CONSENSUS.
The program analyzes consensus results at specific positions within aligned molecular sequences.
Supports molecular alphabets with up to four symbols, including standard DNA and ambiguity codes.

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Main Results:

The CONSENSUS program facilitates the analysis and comparison of different consensus calculation methods.
Its output is suitable for exploratory data analysis.
Enables the selection of optimal thresholds or confidence levels for consensus methods.

Conclusions:

The CONSENSUS program offers a valuable tool for molecular biologists to better understand and apply consensus sequence calculation methods.
Improves the rigor and selection process for consensus determination in sequence analysis.