GENOMEINSPECTOR - A NEW APPROACH TO DETECT CORRELATION PATTERNS OF ELEMENTS ON GENOMIC SEQUENCES

Motivation: Most of the sequences determined in current genome sequenc ing projects remain at least partially unannotated. The available soft ware for DNA sequence analysis is usually limited to the prediction of individual elements (level 1 methods), but does not assess the contex t of different motifs. However the functionality of biological units l ike 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/genomeinspec tor.htm}}, for further analysis of results obtained with level I metho ds (e.g MatInspector {{http://www.gsf.de/biodvlmatinspector.html}} or ConsInspector {{http://www.gsf.de/biodv/consinspector.htm}}). One of t he main features of this modular program is its ability to assess dist ance correlations between large sets of sequence elements which can be used for the identification and definition of basic patterns of funct ional units. The program provides an easy-to-use graphical user interf ace with direct comprehensive display of all results for megabase sequ ences. Sequence elements showing spatial correlations can be easily ex tracted and traced back to the nucleotide sequence with the program. G enomeInspector identified promoters of glycolytic enzymes in yeast {{h ttp:/www.mips.biochem.mpg.de/mips/yeast}} as members of a subgroup wit h unusual location of an ABF1 site. Solely on the basis of distance co rrelation analysis, the program correctly selected those transcription factors within these promoters already known to be involved in the re gulation of glycolytic enzymes, demonstrating the power of this method . Availability: GenomeInspector is available free of charge for non-co mmercial research by anonymous ftp from ariane.gsf.de, directory pub/u nix/genomeinspector/ {{ftp://ariane.gsf.de/pub/unix/genomeinspector/ o r http://ariane.gsf.de/genomeinspector.html}}.