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A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 6, 2014

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.

J D Thompson¹, F Plewniak, O Poch

¹Institut de Génétique et de Biologie Moleculaire et Cellulaire (CNRS/INSERM/ULP), BP 163, 67404 Illkirch Cedex, France. julie@igbmc.u-strasbg.fr

Bioinformatics (Oxford, England)

|March 9, 1999

Summary

This summary is machine-generated.

BAliBASE is a curated database for multiple sequence alignments. It categorizes alignments by conserved regions, aiding in evolutionary and functional studies.

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Area of Science:

Bioinformatics
Computational Biology
Molecular Evolution

Background:

Multiple sequence alignments (MSAs) are fundamental in bioinformatics.
Accurate MSAs are crucial for phylogenetic analysis, protein function prediction, and structural biology.
Existing alignment databases often lack manual refinement and detailed categorization.

Purpose of the Study:

To present BAliBASE, a comprehensive database of manually refined MSAs.
To provide a resource for evaluating alignment methods.
To facilitate research in protein evolution and function.

Main Methods:

Manual refinement of multiple sequence alignments.
Categorization based on core blocks of conservation.
Inclusion of sequence length, similarity, and insertion/extension data.

Main Results:

BAliBASE contains a diverse set of MSAs.
Alignments are systematically categorized by conserved regions and variations.
The database supports the assessment of alignment quality and method performance.

Conclusions:

BAliBASE serves as a valuable, manually curated resource for the scientific community.
It enables rigorous evaluation of multiple sequence alignment algorithms.
Facilitates advancements in understanding protein families and evolutionary relationships.