• An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters.

      Deyneko, Igor V; Weiss, Siegfried; Leschner, Sara; Molecular Immunology, Helmholtz Centre for Infection Research, Inhoffenstr, 7, 38124 Braunschweig, Germany. Igor.Deyneko@helmholtz-hzi.de (2012)
      Transcriptional activity of genes depends on many factors like DNA motifs, conformational characteristics of DNA, melting etc. and there are computational approaches for their identification. However, in real applications, the number of predicted, for example, DNA motifs may be considerably large. In cases when various computational programs are applied, systematic experimental knock out of each of the potential elements obviously becomes nonproductive. Hence, one needs an approach that is able to integrate many heterogeneous computational methods and upon that suggest selected regulatory elements for experimental verification.
    • MatrixCatch--a novel tool for the recognition of composite regulatory elements in promoters.

      Deyneko, Igor V; Kel, Alexander E; Kel-Margoulis, Olga V; Deineko, Elena V; Wingender, Edgar; Weiss, Siegfried; Department of Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany. Igor.Deyneko@helmholtz-hzi.de (2013)
      Accurate recognition of regulatory elements in promoters is an essential prerequisite for understanding the mechanisms of gene regulation at the level of transcription. Composite regulatory elements represent a particular type of such transcriptional regulatory elements consisting of pairs of individual DNA motifs. In contrast to the present approach, most available recognition techniques are based purely on statistical evaluation of the occurrence of single motifs. Such methods are limited in application, since the accuracy of recognition is greatly dependent on the size and quality of the sequence dataset. Methods that exploit available knowledge and have broad applicability are evidently needed.