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Updated: Jun 21, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.
Fabian Schreiber1, Kerstin Pick, Dirk Erpenbeck
1Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany. fab.schreiber@gmail.com
BMC Bioinformatics
|July 18, 2009
Summary
OrthoSelect automates the identification of orthologous gene sequences from expressed sequence tags (ESTs), significantly improving phylogenomic data set creation. This tool accurately detects orthologs, offering a valuable, free solution for researchers working with large EST datasets.
Area of Science:
- Bioinformatics
- Evolutionary Biology
- Genomics
Background:
- Phylogenetic studies increasingly rely on expressed sequence tags (ESTs) for evolutionary insights.
- Manual processing of large, error-prone EST datasets for orthology detection is time-consuming.
- Automated tools are essential for efficient identification of orthologous sequences in phylogenomics.
Purpose of the Study:
- To develop a user-friendly software pipeline for automated construction of phylogenomic data sets from ESTs.
- To facilitate the identification, selection, and alignment of orthologous sequences for phylogenetic analysis.
- To provide a flexible tool adaptable for both novice and expert users in bioinformatics.
Main Methods:
- Developed a software pipeline (OrthoSelect) for processing assembled EST sequences.
- Utilized databases of orthologous groups (OGs) for sequence assignment and translation.
- Implemented automated steps for redundancy elimination, multiple sequence alignment, and refinement (homoplasy exclusion, conserved region selection).
Main Results:
- OrthoSelect accurately identifies orthologous sequences in EST libraries with 98% specificity.
- The tool detected 4% more orthologous sequences compared to a manually curated dataset.
- OrthoSelect provides results consistent with other programs but with significant speedup and added functionalities.
Conclusions:
- OrthoSelect is a highly accurate, automated, and freely available tool for generating orthologous gene alignments from ESTs.
- It significantly accelerates and enhances the process of creating data sets for phylogenomic analyses.
- This tool is valuable for researchers dealing with large EST datasets in phylogenomics.
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