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Towards detection of orthologues in sequence databases
Y P Yuan1, O Eulenstein, M Vingron
1Biocomputing, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69012 Heidelberg, Germany.
Bioinformatics (Oxford, England)
|June 6, 1998
Summary
Distinguishing gene orthologues and paralogues is crucial for understanding evolutionary relationships. This study presents a novel web-based method to reconcile gene and species trees, accurately predicting orthologues and paralogues from BLAST results.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Genetics
Background:
- Identifying homologous sequences using BLAST is common, but multigene families complicate evolutionary analysis.
- Accurate discrimination between orthologues and paralogues is essential for functional assignment and understanding evolutionary divergence.
Purpose of the Study:
- To develop a computational method for distinguishing orthologues from paralogues within large sets of homologous sequences.
- To provide a user-friendly web interface for analyzing BLAST results and inferring gene duplication events.
Main Methods:
- Constructing a reconciled gene tree by comparing a gene tree with the corresponding species phylogenetic tree.
- Parsing BLAST outputs, performing multiple sequence alignments (global or local), and generating bootstrapped trees.
- Inferring gene duplication events when gene and species trees show discrepancies to compute a reconciled tree.
Main Results:
- A web-based tool was developed to automate the analysis of BLAST outputs.
- The method successfully constructs reconciled trees, differentiating between orthologues and paralogues.
- Predicted orthologues and paralogues are clearly indicated in the computed reconciled tree.
Conclusions:
- The developed method effectively resolves ambiguities in homologous sequence classification arising from gene duplication events.
- This approach aids in accurate functional annotation and the study of genome evolution.
- The web interface facilitates broader accessibility for researchers needing to differentiate orthologues and paralogues.
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