PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences.

Microbial Informatics and Experimentation
Jan MrázekAryabrata Basu

Abstract

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. 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...Continue Reading

References

May 7, 1992·Nature·S G OliverP Benit
Apr 16, 1987·Nature·L E Ulanovsky, E N Trifonov
Jul 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·E N Trifonov, J L Sussman
Jul 28, 1995·Science·R D FleischmannJ M Merrick
Dec 2, 1998·Journal of Biomolecular Structure & Dynamics·H HerzelE N Trifonov
Aug 25, 2000·Genome Research·A Bolshoy, E Nevo
Jul 19, 2002·FEBS Letters·Ryoiti Kiyama, Edward N Trifonov
Oct 13, 2004·Journal of Molecular Biology·Patrick Schieg, Hanspeter Herzel
Jul 19, 2005·Nucleic Acids Research·Michael Y TolstorukovVictor B Zhurkin
May 9, 2006·Nucleic Acids Research·Limor Kozobay-AvrahamAlexander Bolshoy
Jul 25, 2006·Nature·Eran SegalJonathan Widom
Feb 14, 2007·BMC Molecular Biology·Hanni Willenbrock, David W Ussery
May 9, 2007·Proceedings of the National Academy of Sciences of the United States of America·Jan MrázekApurva Shah
Feb 24, 2009·Molecular Biology and Evolution·Jan Mrázek
Oct 30, 2009·Nature·Remo RohsBarry Honig

❮ Previous
Next ❯

Citations

Jul 25, 2014·Nucleic Acids Research·Robert LehmannHanspeter Herzel
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Imen MessaoudiZied Lachiri
Aug 5, 2017·Frontiers in Microbiology·Sagar M UtturkarSteven D Brown

❮ Previous
Next ❯

Datasets Mentioned

BETA
MJ0784

Software Mentioned

PerScan
Periodicity Scan ( PerScan )
blastp
Periodicity Plot ( PerPlot )
PerPlot
Apache
Redhat
Genome Randomizer

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.