Parsing regulatory DNA: general tasks, techniques, and the PhyloGibbs approach.
J Biosci
;
2007 Aug; 32(5): 863-70
Article
in English
| IMSEAR
| ID: sea-110816
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.
Full text:
Available
Index:
IMSEAR (South-East Asia)
Main subject:
Software
/
Humans
/
DNA
/
Molecular Sequence Data
/
Base Sequence
/
Regulatory Sequences, Nucleic Acid
/
Sequence Analysis, DNA
/
Computational Biology
/
Regulatory Elements, Transcriptional
/
Animals
Type of study:
Prognostic study
Language:
English
Journal:
J Biosci
Year:
2007
Type:
Article
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