CDH

The Co-regulation Data Harvester (CDH) is a software tool designed to assist with gene annotation in the context of transcriptome data in the model organism Tetrahymena thermophila. Identifying co-regulated genes provides a useful approach for defining pathway-specific machinery in an organism. However, this approach relies on thorough genome annotation, which is a much slower process than genome sequencing per se. Tetrahymena thermophila is a unicellular eukaryote that has been a useful model organism, but it has a fully sequenced but sparsely annotated genome.

To address this issue, the CDH was developed as an automated approach to gene annotation. It begins with a gene of interest and identifies co-regulated genes by accessing the Tetrahymena transcriptome database. Using reciprocal BLAST searches, the tool then identifies closely related genes (orthologs) in other organisms. Finally, it collates the annotations of those orthologs' functions, which provides the user with information to help predict the cellular role of the initial query.

The CDH is freely available and represents a powerful new tool for analyzing cell biological pathways in Tetrahymena. Moreover, to the extent that genes and pathways are conserved between organisms, the inferences obtained via the CDH should be relevant and can be explored in many other systems. This makes it a valuable resource for researchers working in diverse areas of biology.