An optimized protocol for analysis of EST sequences

The vast body of Expressed Sequence Tag (EST) data in the public databases provide an important resource for comparative and functional genomics studi es and an invaluable tool for the annotation of genomic sequences. We have developed a rigorous protocol for reconstructing the sequences of transcrib ed genes from EST and gene sequence fragments. A key element in developing this protocol has been the evaluation of a number of sequence assembly prog rams 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 demonstrate d their utility in a variety of applications and are freely available to th e scientific research community.