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Nucleic Acids Research 2005 33(Database Issue):D71-D74; doi:10.1093/nar/gki064
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Nucleic Acids Research, 2005, Vol. 33, Database issue D71-D74
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes

Y. Lee*, J. Tsai, S. Sunkara, S. Karamycheva, G. Pertea, R. Sultana, V. Antonescu, A. Chan, F. Cheung and J. Quackenbush

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

* To whom correspondence should be addressed. Tel: +1 301 795 7831; Fax: +1 301 838 0208; Email: dlee{at}tigr.org

Received September 14, 2004; Revised and Accepted October 5, 2004

Although the list of completed genome sequencing projects has expanded rapidly, sequencing and analysis of expressed sequence tags (ESTs) remain a primary tool for discovery of novel genes in many eukaryotes and a key element in genome annotation. The TIGR Gene Indices (http://www.tigr.org/tdb/tgi) are a collection of 77 species-specific databases that use a highly refined protocol to analyze gene and EST sequences in an attempt to identify and characterize expressed transcripts and to present them on the Web in a user-friendly, consistent fashion. A Gene Index database is constructed for each selected organism by first clustering, then assembling EST and annotated cDNA and gene sequences from GenBank. This process produces a set of unique, high-fidelity virtual transcripts, or tentative consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to genetic and physical maps, to provide links to orthologous and paralogous genes, and as a resource for comparative and functional genomic analysis.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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