%0 Journal Article
%T PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
%A Jan Mr¨˘zek
%A Tejas Chaudhari
%A Aryabrata Basu
%J Microbial Informatics and Experimentation
%D 2011
%I BioMed Central
%R 10.1186/2042-5783-1-13
%X 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.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.Most naturally occurring DNA sequences feature two strong periodic patterns. The first relates to a 3 bp period resulting from amino acid and codon usage biases in protein coding genes. The second arises from periodic spacing of A-tracts (short runs of A or T) phased with the DNA helical period of ~10.5 bp. The periodically spaced A-tracts are a primary indicator of intrinsically bent DNA and the main component of nucleosome positioning signals in eukaryotes [1-3]. Similar periodic patterns are present in prokaryotes, where they could contribute to DNA packaging in the nucleoid [4,5], promote the appropriate mode of supercoiling [6,7], and/or facilitate the initiation and termination of transcription [8,9]. There are significant differences in the character and intensity of these periodic patterns among different genomes as well as among different segments of the same genome [4,6,7,10]. In some species, the intragenomic heterogeneity of the sequence periodicity has been linked to local variance in gene expression and chromatin structure [4,11,12].Despite the biological significance of DNA curvature-related sequence periodicity, there are virtual
%K Software
%K Genome
%K Chromosome
%K DNA structure
%K Nucleoid
%K Chromatin
%K A-tracts
%K Periodic spacing
%K Gene expression
%U http://www.microbialinformaticsj.com/content/1/1/13