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Updated: Jul 10, 2026
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
OPTIC: orthologous and paralogous transcripts in clades.
Andreas Heger1, Chris P Ponting
1Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, Le Gros Clark Building, Oxford OX1 3QX, UK.
Nucleic Acids Research
|October 16, 2007
Summary
The Orthologous and Paralogous Transcripts in Clades (OPTIC) database offers gene predictions and orthology assignments for multiple species across three clades. This resource facilitates comparative genomics across evolutionary lineages.
Area of Science:
- Comparative genomics
- Bioinformatics
- Evolutionary biology
Background:
- Advancements in sequencing technology have generated a wealth of metazoan genome data.
- Comparative genomic studies are expanding from pairwise comparisons to whole clade analyses.
Purpose of the Study:
- To establish a comprehensive database of orthologous and paralogous transcripts across multiple species within defined clades.
- To provide accessible gene predictions, orthology assignments, and related data for evolutionary and functional genomic research.
Main Methods:
- Development of the Orthologous and Paralogous Transcripts in Clades (OPTIC) database.
- Inclusion of gene predictions and orthology assignments for three distinct clades: amniotes, Drosophila, and nematodes.
- Generation of multiple alignments and phylogenetic trees for the identified orthologous groups.
Main Results:
- The OPTIC database currently hosts data for 17,443 orthologous groups in amniotes, 12,889 in Drosophila, and 13,626 in nematodes.
- Gene predictions, alignments, and phylogenetic trees are available for browsing and download.
- The database is designed for future expansion with additional genomes and clades.
Conclusions:
- The OPTIC database serves as a valuable resource for large-scale comparative genomic analyses.
- Facilitates research into gene evolution, function, and conservation across diverse metazoan lineages.
- Supports ongoing and future genomic research by providing curated, downloadable data sets.
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