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rVISTA 2.0 [electronic resource] : Evolutionary Analysis of Transcription Factor Binding Sites

Published
Washington, D.C. : United States. Dept. of Energy, 2004.
Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy.
Physical Description
PDF-file: 18 pages; size: 0.5 Mbytes
Additional Creators
Lawrence Berkeley National Laboratory, United States. Department of Energy, and United States. Department of Energy. Office of Scientific and Technical Information
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Summary
Identifying and characterizing the patterns of DNA cis-regulatory modules represents a challenge that has the potential to reveal the regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory modules are under positive selection and therefore are often conserved between related species. Using this evolutionary principle we have created a comparative tool, rVISTA, for analyzing the regulatory potential of noncoding sequences. The rVISTA tool combines transcription factor binding site (TFBS) predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are highly conserved and present in a specific configuration within an alignment. Here we present the newly developed version 2.0 of the rVISTA tool that can process alignments generated by both zPicture and PipMaker alignment programs or use pre-computed pairwise alignments of seven vertebrate genomes available from the ECR Browser. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences. rVISTA tool is publicly available at http://rvista.dcode.org/.
Report Numbers
E 1.99:ucrl-jrnl-202112
ucrl-jrnl-202112
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Note
Published through SciTech Connect.
01/28/2004.
"ucrl-jrnl-202112"
Published in: Nucleic Acids Research, vol. 32, Web Server, July 1, 2004, pp. 217-21 32 ISSN 0305-1048; NARHAD FT
Ovcharenko, I; Loots, G G.
Funding Information
W-7405-ENG-48
View MARC record | catkey: 13810319