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Bortoluzzi, Stefania and Coppe, Alessandro and Bisognin, Andrea and Pizzi, Cinzia and Danieli, Gian Antonio (2005) A multistep bioinformatic approach detects putative regulatory elements in gene promoters. [Online journal papers]

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Per gentile concessione di: http://www.biomedcentral.com/1471-2105/6/121

Abstract (english)

Background

Searching for approximate patterns in large promoter sequences frequently produces an exceedingly high numbers of results. Our aim was to exploit biological knowledge for definition of a sheltered search space and of appropriate search parameters, in order to develop a method for identification of a tractable number of sequence motifs.
Results

Novel software (COOP) was developed for extraction of sequence motifs, based on clustering of exact or approximate patterns according to the frequency of their overlapping occurrences. Genomic sequences of 1 Kb upstream of 91 genes differentially expressed and/or encoding proteins with relevant function in adult human retina were analyzed. Methodology and results were tested by analysing 1,000 groups of putatively unrelated sequences, randomly selected among 17,156 human gene promoters. When applied to a sample of human promoters, the method identified 279 putative motifs frequently occurring in retina promoters sequences. Most of them are localized in the proximal portion of promoters, less variable in central region than in lateral regions and similar to known regulatory sequences. COOP software and reference manual are freely available upon request to the Authors.
Conclusion

The approach described in this paper seems effective for identifying a tractable number of sequence motifs with putative regulatory role.


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EPrint type:Online journal papers
Anno di Pubblicazione:2005
Key Words:sequence motifs, putative regulatory
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/18 Genetica
Struttura di riferimento:Dipartimenti > Dipartimento di Ingegneria dell'Informazione
Dipartimenti > Dipartimento di Biologia
Codice ID:1192
Depositato il:09 Dec 2008
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