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dc.contributor.authorMrázek, Jan
dc.contributor.authorChaudhari, Tejas
dc.contributor.authorBasu, Aryabrata
dc.date.accessioned2013-06-12T14:55:53Z
dc.date.available2013-06-12T14:55:53Z
dc.date.issued2011-11-28
dc.identifier.citationMicrobial Informatics and Experimentation. 2011 Nov 28;1(1):13
dc.identifier.urihttp://dx.doi.org/10.1186/2042-5783-1-13
dc.identifier.urihttp://hdl.handle.net/10724/19610
dc.description.abstractAbstract Background Periodic spacing of short adenine or thymine runs phased with DNA helical period of ~10.5 bp is associated with intrinsic DNA curvature and deformability, which play important roles in DNA-protein interactions and in the organization of chromosomes in both eukaryotes and prokaryotes. Local differences in DNA sequence periodicity have been linked to differences in gene expression in some organisms. Despite the significance of these periodic patterns, there are virtually no publicly accessible tools for their analysis. Results We present novel tools suitable for assessments of DNA curvature-related sequence periodicity in nucleotide sequences at the genome scale. Utility of the present software is demonstrated on a comparison of sequence periodicities in the genomes of Haemophilus influenzae, Methanocaldococcus jannaschii, Saccharomyces cerevisiae, and Arabidopsis thaliana. The software can be accessed through a web interface and the programs are also available for download. Conclusions The present software is suitable for comparing DNA curvature-related sequence periodicity among different genomes as well as for analysis of intrachromosomal heterogeneity of the sequence periodicity. It provides a quick and convenient way to detect anomalous regions of chromosomes that could have unusual structural and functional properties and/or distinct evolutionary history.
dc.titlePerPlot & PerScan: Tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
dc.typeJournal Article
dc.date.updated2013-06-07T14:01:22Z
dc.description.versionPeer Reviewed
dc.language.rfc3066en
dc.rights.holderJan Mrázek et al.; licensee BioMed Central Ltd.


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