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Nucleic Acids Research, 2000, Vol. 28, No. 18 3657-3665
© 2000 Oxford University Press

An optimized protocol for analysis of EST sequences

Feng Liang, Ingeborg Holt, Geo Pertea, Svetlana Karamycheva, Steven L. Salzberg and John Quackenbush*

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

The vast body of Expressed Sequence Tag (EST) data in the public databases provide an important resource for comparative and functional genomics studies and an invaluable tool for the annotation of genomic sequences. We have developed a rigorous protocol for reconstructing the sequences of transcribed genes from EST and gene sequence fragments. A key element in developing this protocol has been the evaluation of a number of sequence assembly programs to determine which most faithfully reproduce transcript sequences from EST data. The TIGR Gene Indices constructed using this protocol for human, mouse, rat and a variety of other plant and animal models have demonstrated their utility in a variety of applications and are freely available to the scientific research community.

* To whom correspondence should be addressed. Tel: +1 301 838 3528; Fax: +1 301 838 0208; Email: johnq@tigr.org


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