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Bioinformatics Advance Access originally published online on July 15, 2009
Bioinformatics 2009 25(19):2603-2604; doi:10.1093/bioinformatics/btp436
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

DiProGB: the dinucleotide properties genome browser

Maik Friedel 1,*, Swetlana Nikolajewa 2, Jürgen Sühnel 1 and Thomas Wilhelm 3,*

1Biocomputing Group, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena Centre for Bioinformatics, Beutenbergstr. 11, 2Systems Biology/Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena Centre for Bioinformatics, Beutenbergstr. 11a, 07745 Jena, Germany and 3Theoretical Systems Biology, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: DiProGB is an easy to use new genome browser that encodes the primary nucleotide sequence by thermodynamical and geometrical dinucleotide properties. The nucleotide sequence is thus converted into a sequence graph. This visualization, supported by different graph manipulation options, facilitates genome analyses, because the human brain can process visual information better than textual information. Also, DiProGB can identify genomic regions where certain physical properties are more conserved than the nucleotide sequence itself. Most of the DiProGB tools can be applied to both, the primary nucleotide sequence and the sequence graph. They include motif and repeat searches as well as statistical analyses. DiProGB adds a new dimension to the common genome analysis approaches by taking into account the physical properties of DNA and RNA.

Availability and Implementation: Source code and binaries are freely available for download at http://diprogb.fli-leibniz.de, implemented in C++ and supported on MS Windows and Linux (using e.g. WineHQ).

Contact: maikfr{at}fli-leibniz.de; thomas.wilhelm{at}bbsrc.ac.uk

Associate Editor: Dmitrij Frishman

Received on April 7, 2009; revised on June 17, 2009; accepted on July 12, 2009

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