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Multiple non-collinear TF-map alignments of promoter regions

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dc.contributor.author Blanco, Enrique
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Messeguer, Xavier
dc.contributor.other Universitat Pompeu Fabra
dc.date.accessioned 2011-10-26T11:07:52Z
dc.date.available 2011-10-26T11:07:52Z
dc.date.issued 2007
dc.identifier.citation Blanco E, Guigó R, Messeguer X. Multiple non-collinear TF-map alignments of promoter regions. BMC Bioinformatics. 2007; 8: 138. DOI 10.1186/1471-2105-8-138
dc.identifier.issn 1471-2105
dc.identifier.uri http://hdl.handle.net/10230/12926
dc.description.abstract Background: The analysis of the promoter sequence of genes with similar expression patterns is/na basic tool to annotate common regulatory elements. Multiple sequence alignments are on the/nbasis of most comparative approaches. The characterization of regulatory regions from coexpressed/ngenes at the sequence level, however, does not yield satisfactory results in many/noccasions as promoter regions of genes sharing similar expression programs often do not show/nnucleotide sequence conservation./nResults: In a recent approach to circumvent this limitation, we proposed to align the maps of/npredicted transcription factors (referred as TF-maps) instead of the nucleotide sequence of two/nrelated promoters, taking into account the label of the corresponding factor and the position in the/nprimary sequence. We have now extended the basic algorithm to permit multiple promoter/ncomparisons using the progressive alignment paradigm. In addition, non-collinear conservation/nblocks might now be identified in the resulting alignments. We have optimized the parameters of/nthe algorithm in a small, but well-characterized collection of human-mouse-chicken-zebrafish/northologous gene promoters./nConclusion: Results in this dataset indicate that TF-map alignments are able to detect high-level/nregulatory conservation at the promoter and the 3'UTR gene regions, which cannot be detected/nby the typical sequence alignments. Three particular examples are introduced here to illustrate the/npower of the multiple TF-map alignments to characterize conserved regulatory elements in/nabsence of sequence similarity. We consider this kind of approach can be extremely useful in the/nfuture to annotate potential transcription factor binding sites on sets of co-regulated genes from/nhigh-throughput expression experiments.
dc.language.iso eng
dc.publisher BioMed Central
dc.rights © 2007 Blanco et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is also available from: http://www.biomedcentral.com/1471-2105/8/138
dc.rights.uri http://creativecommons.org/licenses/by/2.0/
dc.subject.other Factors de transcripció
dc.subject.other Genètica -- Tècnica
dc.title Multiple non-collinear TF-map alignments of promoter regions
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1471-2105-8-138
dc.subject.keyword Promoter regions
dc.subject.keyword Nucleotide sequence
dc.subject.keyword TF-map alignment
dc.subject.keyword Non-collinear conservation blocks
dc.subject.keyword 3'UTR
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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