Format

Send to

Choose Destination
Bioinformatics. 2009 Oct 1;25(19):2603-4. doi: 10.1093/bioinformatics/btp436. Epub 2009 Jul 15.

DiProGB: the dinucleotide properties genome browser.

Author information

1
Biocomputing Group, Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena Centre for Bioinformatics, Beutenbergstr. 11, Jena, Germany. maikfr@fli-leibniz.de

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).

PMID:
19605418
PMCID:
PMC2752610
DOI:
10.1093/bioinformatics/btp436
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center