Genomelnspector: a new approach to detect correlation patterns of elements on genomic sequences
Institut für Saugetiergenetik, GSF-Forschungszentrum für Umwelt und Gesundheit GmbH Ingolstädter Landstraße 1, D-85758 Oberschleißheim, Germany
1To whom correspondence should be addressed
MOTIVATION: Most of the sequences determined in current genome sequencing projects remain at least partially unannotated. The available software for DNA sequence analysis is usually limited to the prediction of individual elements (level 1 methods), but does not assess the context of different motifs. However, the functionality of biological units like promoters depends on the correct spatial organization of multiple individual elements.
RESULTS: Here, we present a second-level software package called GenomeInspector {{http://www.gsf.de/biodv/genomeinspector.html}}, for further analysis of results obtained with level 1 methods (e.g. MatInspector {{http://www.gsf.de/biodv/matinspector.html}} or ConsInspector {{http://www.gsf.de/biodv/consInspector.html}}). One of the main features of this modular program is its ability to assess distance correlations between large sets of sequence elements which can be used for the identification and definition of basic patterns of functional units. The program provides an easy-to-use graphical user interface with direct comprehensive display of all results for megabase sequences. Sequence elements showing spatial correlations can be easily extracted and traced back to the nucleotide sequence with the program. GenomeInspector identified promoters of glycolytic enzymes in yeast {{http://www.mips.biochem.mpg.de/mips/yeast/}} as members of a subgroup with unusual location of an ABFI site. Solely on the basis of distance correlation analysis, the program correctly selected those transcription factors within these promoters already known to be involved in the regulation of glycolytic enzymes, demonstrating the power of this method.
AVAILABILITY: GenomeInspector is available free of charge for non-commercial research by anonymous ftp from ariane.gsf.de, directory pub/unix/genomeinspector/ {{ftp://ariane.gsf.de/pub/unix/genomeinspector/ or http:/ariane.gsf.de/genomeinspector.html}}.
CONTACT: quandt{at}gsf.de or werner{at}gsf.de
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