ArticleGenome biology2002
JEvTrace: refinement and variations of the evolutionary trace in JAVA.
Article in Genome biology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.Nucleic acids research · 2016Article
- Recent advances in functional region prediction by using structural and evolutionary information - Remaining problems and future extensions.Computational and structural biotechnology journal · 2013Review
- The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate.BMC genomics · 2011Article
- Meet me halfway: when genomics meets structural bioinformatics.Journal of cardiovascular translational research · 2011Article
- Visualization of multiple alignments, phylogenies and gene family evolution.Nature methods · 2010Review
- A statistical phylogeography of influenza A H5N1.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.PLoS biology · 2007Article
- Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDetails of functional speciation within gene families can be difficult to identify using standard multiple sequence alignment (MSA) methods. The evolutionary trace (ET) was developed as a visualization tool to combine MSA, phylogenetic and structural data for identification of functional sites in proteins. The method has been successful in extracting evolutionary details of functional surfaces in a number of biological systems and modifications of the method are useful in creating hypotheses about the function of previously unannotated genes. We wish to facilitate the graphical interpretation of disparate data types through the creation of flexible software implementations.
resultsWe have implemented the ET method in a JAVA graphical interface, JEvTrace. Users can analyze and visualize ET input and output with respect to protein phylogeny, sequence and structure. Function discovery with JEvTrace is demonstrated on two proteins with recently determined crystal structures: YlxR from Streptococcus pneumoniae with a predicted RNA-binding function, and a Haemophilus influenzae protein of unknown function, YbaK. To facilitate analysis and storage of results we propose a MSA coloring data structure. The sequence coloring format readily captures evolutionary, biological, functional and structural features of MSAs.
conclusionsProtein families and phylogeny represent complex data with statistical outliers and special cases. The JEvTrace implementation of the ET method allows detailed mining and graphical visualization of evolutionary sequence relationships.
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