Parsing regulatory DNA: General tasks, techniques, and the PhyloGibbs approach View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2007-08

AUTHORS

Rahul Siddharthan

ABSTRACT

In this review, we discuss the general problem of understanding transcriptional regulation from DNA sequence and prior information. The main tasks we discuss are predicting local regions of DNA, cis-regulatory modules (CRMs) that contain binding sites for transcription factors (TFs), and predicting individual binding sites. We review various existing methods, and then describe the approach taken by PhyloGibbs, a recent motif-finding algorithm that we developed to predict TF binding sites, and PhyloGibbs-MP, an extension to PhyloGibbs that tackles other tasks in regulatory genomics, particularly prediction of CRMs. More... »

PAGES

863-870

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s12038-007-0086-0

DOI

http://dx.doi.org/10.1007/s12038-007-0086-0

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1008642435

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17914228


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