PRESTA associating promoter sequences with information on gene expression 英文参考文献.docVIP

/2002/3/9/research/0050.1 Research PRESTA: associating promoter sequences with information on gene expression Václav Mach Address: Institute of Entomology, Czech Academy of Sciences, Branisovská 31, 370 05 Ceské Budejovice, Czech Republic. E-mail: mach@entu.cas.cz Published: 21 August 2002 Received: 8 January 2002 Revised: 12 April 2002 Accepted: 24 June 2002 GenomeBiology 2002, 3(9):research0050.1–0050.7 The electronic version of this article is the complete one and can be found online at /2002/3/9/research/0050 ? 2002 Mach, licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: Large sets of well-characterized promoter sequences are required to facilitate the understanding of promoter architecture. The major sequence databases are a prospective source of upstream regulatory regions, but suffer from inaccurate annotation. The software tool PRESTA (PRomoter EST Association) presented in this study is designed for efficient recovery of characterized and partially verified promoters from GenBank and EMBL libraries. Results: The PRESTA algorithm examines the putative GenBank/EMBL promoters and automatically removes most of the poorly annotated entries. The remaining records are connected to expressed sequence tags (ESTs) through a high-stringency BLAST search. The frequency and source of recovered ESTs provide an estimate of the activity and expression pattern of the promoter, and the ESTs’ 5′ ends assist in transcription start-site verification. The PRESTA database provides easy access to non-redundant upstream regulatory regions recently extracted by the PRESTA algorithm. The current size of this resource is 552 human and 241 mouse promoters. Surprisingly, no overlap between the PRESTA database and the Eukaryotic Promoter Database (EPD) was detected by sequence comparison. Conclusions: The PRESTA