Exceptional Chromosome Regions Workshop I



Reconstruction and Annotation of Transcribed Sequences: The TIGR Gene Indices

John Quackenbush, Ingeborg Holt, Feng Liang, Geo Pertea, Jonathan Upton, and Thomas S. Hansen
The Institute for Genomic Research, Rockville, MD 20850

A goal of the Human Genome Project is identification of the complete set of human genes and the role played by these genes in development and disease. The sequencing of Expressed Sequence Tags (ESTs) has provided a first glimpse of the collection of transcribed sequences in humans and other organisms, but significant additional information can be obtained by a thorough analysis of the EST data. TIGR's analysis of the world's collection of EST sequence data, captured in our Gene Indices, provides assembled consensus sequences that are of high confidence and represent our best estimate of the collection of transcribed sequences underlying the ESTs. In addition to the Human Gene Index (HGI), we maintain Gene Indices for a variety of other species, including mouse, rat, Drosophila, zebrafish, rice, tomato, and Arabidopsis. Collectively, the Gene Indices represent a unique resource for the comparative analysis of mammalian genes and may provide insight into gene function, regulation, and evolution.

We have recently expanded the TIGR Gene Index project to include quarterly releases, expanded annotation, integration with mapping and genomic sequence data, and more robust search capabilities. In addition, we are developing a database of mammalian orthologues based on comparison of the human, mouse, and rat TC sequences and a web-based presentation to allow the data to be effectively explored. This database will provide direct links between the human, mouse, and rat assemblies and represent the most extensive catalog of eukaryotic orthologues available, providing a valuable resource for gene identification, elucidation of functional domains, and analysis of gene and genome evolution.

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