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Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability
E Depiereux1, G Baudoux, P Briffeuil
1Department of Biology, Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium. eric.depiereux@fundp.ac.be
Computer Applications in the Biosciences : CABIOS
|June 1, 1997
Summary
Match-Box software identifies conserved protein regions using statistical thresholds, bypassing traditional gap penalties. This method aids in protein structure modeling, mutagenesis, and gene cloning via PCR.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Match-Box software offers protein sequence alignment tools.
- It utilizes strict statistical thresholds for segment similarity.
- The method does not require gap penalties, treating gaps as alignment outcomes.
Purpose of the Study:
- To present the Match-Box software for protein sequence analysis.
- To highlight its utility in homology modeling, mutagenesis, and gene cloning.
- To provide a novel approach to protein sequence alignment.
Main Methods:
- Protein sequence alignment based on statistical similarity thresholds.
- Gaps are a result of alignment, not a predefined parameter.
- A reliability score is calculated by progressively increasing similarity thresholds.
Main Results:
- The method demonstrates reliable results on protein families with known structures and low sequence similarity.
- A reliability score is computed to assess alignment quality.
- Scores are displayed below aligned sequences for detailed analysis.
Conclusions:
- Match-Box provides reliable identification of conserved protein regions.
- The software is valuable for various applications in molecular biology and bioinformatics.
- It offers an alternative alignment strategy relevant for homology modeling and genetic engineering.