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Related Experiment Video

Updated: Feb 9, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.

Ian T Fiddes^1,2, Joel Armstrong¹, Mark Diekhans¹

¹Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA.

Genome Research

|June 10, 2018

Summary

The Comparative Annotation Toolkit (CAT) enables robust genome annotation and orthology identification for diverse species. This open-source tool facilitates the discovery of novel genes and variants across multiple genomes.

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Area of Science:

Genomics
Bioinformatics

Background:

Advancements in sequencing technologies have led to a surge in de novo genome assemblies.
Robust genome annotation methods are crucial for comparing these new assemblies.

Purpose of the Study:

To introduce the Comparative Annotation Toolkit (CAT), an open-source tool for efficient and flexible genome annotation.
To demonstrate CAT's utility in annotating diverse genomes and identifying orthology relationships.

Main Methods:

Development and application of the Comparative Annotation Toolkit (CAT).
Simultaneous annotation of entire clades and identification of orthology relationships.
Application to rat, great ape, diverse mammal, and personal human genomes.

Main Results:

CAT successfully improved annotations on the rat genome.
Enabled annotation of great apes, diverse mammals, and diploid human genomes.
Facilitated the discovery of novel genes, isoforms, and structural variants, even in well-studied genomes.

Conclusions:

The Comparative Annotation Toolkit (CAT) provides a flexible and robust solution for comparative genome annotation.
CAT enhances the discovery of genomic features and improves cross-species RNA expression analysis.