NOTE:Effective 15 January 2008, VBI's hosting and support of the ESTAP application is discontinued and login to this page will be disabled. The ESTAP application and documentation will continue to be available for download on a best-effort basis.

ESTAP (EST Analysis Pipeline) is a series of automated procedures that verify, store and analyze EST (Expressed Sequence Tag) data generated using high-throughput platforms. The Web-accessible ESTAP software provides EST analysis support to a distributed group of researchers working on a variety of target organisms (Mao C, Cushman JC, May GD, Weller JW. ESTAP - an automated system for the analysis of EST data. Bioinformatics 2003; 19:1720-1722).

ESTAP automatically cleanses raw sequence data by removing vector, low quality, and contaminating sequences. The cleansed sequences are compared to a set of DNA or protein databases using the BLAST algorithms. ESTAP also clusters and assembles EST collections into singlet and contig (redundant) datasets using d2_cluster and CAP3. The function of the singlets and contigs can be automatically annotated using the InterProScan program from the European Bioinformatics Institute (EBI). The raw and cleansed data and analysis results are stored in a relational database. ESTAP affords easy viewing of the original data, the cleansed data, and the analysis results via a Web browser. It also allows the data owner to automatically prepare and submit selected sequences to dbEST. Beyond the scope of EST projects, ESTAP is able to handle sequences from small-scale genomic DNA libraries. It can clean, BLAST and assemble the genomic DNA sequences.

ESTAP is a co-development software project supported by the Samuel Roberts Noble Foundation in Ardmore Oklahoma, the University of Nevada at Reno and the Virginia Bioinformatics Institute. To view publicly available EST sequences from the Ice Plant database, fill in the boxes to the left with: login: Mesem1, password: Mesem1. To view publicly available EST sequences from wine grape (Vitis vinifera) database use login: Vitis1, password: Vitis1. To view publicly available Phytophthora EST sequences from the Phytophthora Genome Consortium, use login: Phytophthora, password: Phytophthora. To view publicly available EST sequences from the Douglas-fir database, fill in the boxes to the left with: login: Douglas-fir, password: Douglas-fir. To view publicly available EST sequences from the wild strawberry (Fragaria vesca) database, fill in the boxes to the left with: login: Fragaria, password: Fragaria.

The following people have contributed to the development of the ESTAP project (alphabetically):
Principal Investigator (Aug. 2000 - Jun. 2002): Jennifer Weller
Principal Investigator (Jul. 2002 - Nov. 2003): Bruno Sobral
Partners/Sponsors: John Cushman (UNR) and Gregory May (Noble), Bruno Sobral (VBI) and Brett Tyler (VBI)
Project Manager/Technical Lead: Chunhong Mao
Programmers: Sheryl Hao (Jul. 2001 - Jul. 2003), Chunhong Mao and Quoc Nguyen (May 2001 - Jan. 2002)
Database Administrators: Olga Brazhnik (Dec. 2000 - Oct. 2001), Paul Toffenetti and Sally Waldon

Acknowledgements and funding sources