Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura | Zendy

Yonatan H. Grad | Zendy; Frederick P. Roth | Zendy; Marc S. Halfon | Zendy; George M. Church | Zendy

Open Access

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura

Author(s) -

Yonatan H. Grad,

Frederick P. Roth,

Marc S. Halfon,

George M. Church

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bth320

Subject(s) - computational biology , biology , drosophila pseudoobscura , enhancer , drosophila melanogaster , cis regulatory module , genome , genetics , genomics , comparative genomics , subsequence , gene , transcription factor , mathematical analysis , mathematics , bounded function

To date, computational searches for cis-regulatory modules (CRMs) have relied on two methods. The first, phylogenetic footprinting, has been used to find CRMs in non-coding sequence, but does not directly link DNA sequence with spatio-temporal patterns of expression. The second, based on searches for combinations of transcription factor (TF) binding motifs, has been employed in genome-wide discovery of similarly acting enhancers, but requires prior knowledge of the set of TFs acting at the CRM and the TFs' binding motifs.

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