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OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences
Fabian Schreiber1, Gert Wörheide, Burkhard Morgenstern
1Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany. Fschrei@gwdg.de
Nucleic Acids Research
|June 4, 2009
Summary
Expressed sequence tags (EST) enable affordable phylogenetic analysis. A new web server automates the detection and alignment of orthologous genes from ESTs, simplifying evolutionary studies.
Area of Science:
- Bioinformatics
- Evolutionary Biology
- Genomics
Background:
- Phylogenetic analyses often rely on orthologous gene sequences, but constructing these datasets is challenging, especially without whole genome data.
- Existing tools for creating phylogenomic datasets are often semi-automated or complex pipelines requiring significant user configuration.
- Expressed sequence tags (ESTs) provide a cost-effective alternative for evolutionary studies when whole genome sequences are unavailable.
Purpose of the Study:
- To develop a fully automated, web-based pipeline for the detection and alignment of orthologous gene sequences from ESTs.
- To simplify the construction of reliable datasets for phylogenomic analyses.
- To provide researchers with an accessible tool for exploring evolutionary history.
Main Methods:
- Development of the OrthoSelect approach for identifying orthologous genes within EST libraries.
- Implementation of a web server to host the OrthoSelect pipeline, enabling user-friendly access.
- Automated processing of EST data to generate orthologous gene alignments.
Main Results:
- The OrthoSelect web server successfully detects orthologous gene sequences in EST libraries.
- The pipeline generates orthologous gene alignments suitable for phylogenomic studies.
- The server offers an extensive results section with visualizations, annotations, and data matrices.
Conclusions:
- The OrthoSelect web server represents the first web-based pipeline for automated EST analysis and orthologous gene alignment.
- This tool significantly simplifies the process of building phylogenomic datasets, making evolutionary studies more accessible.
- The availability of this web server facilitates research into the evolutionary history of organisms using EST data.
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