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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 6, 2014
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
1Bioinformatics Section, Faculty of Sciences, Vrije Universiteit De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands.
Nucleic Acids Research
|June 28, 2005
Summary
PRofile ALIgNEment (PRALINE) is a versatile tool for multiple sequence alignment, enhancing accuracy with homology and secondary structure data. It offers customizable visualization and output formats for researchers.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Multiple sequence alignment is crucial for understanding protein function and evolution.
- Integrating diverse data types can improve alignment accuracy and reliability.
Purpose of the Study:
- To introduce PRofile ALIgNEment (PRALINE), a customizable multiple sequence alignment application.
- To enhance alignment generation by incorporating homology and secondary structure information.
Main Methods:
- PRALINE integrates homology search results for extended alignments.
- It supports seven secondary structure prediction programs for consensus-based structural integration.
- The application offers two interfaces for different user needs.
Main Results:
- PRALINE provides web-based, customizable visualization with multiple color schemes.
- Alignments are available in PDF format for publication.
- Sequence grouping is visualized as a dendrogram.
Conclusions:
- PRALINE offers a flexible and comprehensive solution for multiple sequence alignment.
- Its integration of structural and homology data aids in generating high-confidence alignments.
- The user-friendly interface and visualization options facilitate research and publication.
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