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PRESTA: associating promoter sequences with information on gene expression
1Institute of Entomology, Czech Academy of Sciences, Ceské Budejovice, Czech Republic. mach@entu.cas.cz
Genome Biology
|September 13, 2002
Summary
The PRESTA tool efficiently identifies and verifies promoter sequences from large databases, aiding promoter architecture research. It uses expressed sequence tags (ESTs) to confirm promoter activity and expression patterns.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Accurate promoter sequences are crucial for understanding gene regulation.
- Existing sequence databases contain numerous inaccurately annotated promoter regions.
- There is a need for reliable methods to identify and verify promoters.
Purpose of the Study:
- To develop a computational tool, PRESTA (PRomoter EST Association), for efficient recovery and verification of promoter sequences.
- To create a curated database of characterized and partially verified promoters.
Main Methods:
- The PRESTA algorithm filters GenBank/EMBL promoter entries, removing poorly annotated ones.
- A high-stringency BLAST search links remaining promoters to expressed sequence tags (ESTs).
- EST 5' ends are used to verify transcription start sites and estimate promoter activity.
Main Results:
- PRESTA successfully identifies and verifies promoter sequences, significantly improving data quality.
- The PRESTA database contains 552 human and 241 mouse promoters.
- No overlap was found between the PRESTA database and the Eukaryotic Promoter Database (EPD).
Conclusions:
- The PRESTA algorithm effectively verifies promoters by mapping EST 5' ends.
- The PRESTA database offers a valuable, complementary resource of characterized promoter sequences.
- This work highlights the utility of ESTs for promoter verification and database curation.