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Literature DB >> 14992516

Motif discovery in heterogeneous sequence data.

A Prakash¹, M Blanchette, S Sinha, M Tompa.

Abstract

This paper introduces the first integrated algorithm designed to discover novel motifs in heterogeneous sequence data, which is comprised of coregulated genes from a single genome together with the orthologs of these genes from other genomes. Results are presented for regulons in yeasts, worms, and mammals.

Entities: Species

Mesh：

Year: 2004 PMID： 14992516 DOI： 10.1142/9789812704856_0033

Source DB: PubMed Journal: Pac Symp Biocomput ISSN： 2335-6928

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Cited

30 in total

1. Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.

Authors: Gurmukh Sahota; Gary D Stormo
Journal: Bioinformatics Date: 2010-08-31 Impact factor: 6.937

2. Modulefinder: a tool for computational discovery of cis regulatory modules.

Authors: Anthony A Philippakis; Fangxue Sherry He; Martha L Bulyk
Journal: Pac Symp Biocomput Date: 2005

3. G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis.

Authors: Michael Freeling; Lakshmi Rapaka; Eric Lyons; Brent Pedersen; Brian C Thomas
Journal: Plant Cell Date: 2007-05-11 Impact factor: 11.277

Motif discovery in heterogeneous sequence data.

1. Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.

2. Modulefinder: a tool for computational discovery of cis regulatory modules.

3. G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis.

4. A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction.

Review 5. Identifying regulatory elements in eukaryotic genomes.

6. Recent computational approaches to understand gene regulation: mining gene regulation in silico.

Review 7. Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.

8. The effect of orthology and coregulation on detecting regulatory motifs.

9. Finding regulatory DNA motifs using alignment-free evolutionary conservation information.

Review 10. Integrating sequence, evolution and functional genomics in regulatory genomics.