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Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0

Wittkop, Tobias ; Rahmann, Sven ; Baumbach, Jan

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
We investigated the problem of imprecisely determined prokaryotic transcription factor (TF) binding sites (TFBSs). We found that the identification and reinvestigation of questionable binding motifs may result in improved models of these motifs. Subsequent modelbased predictions of gene regulatory interactions may be performed with increased accuracy when the TFBSs annotation underlying these models has been re-adjusted. We present MoRAine 2.0, a significantly improved version of MoRAine. It can automatically identify cases of unfavorable TFBS strand annotations and imprecisely determined TFBS positions. With release 2.0, we close the gap between reasonable running time and high accuracy. Furthermore, it requires only minimal input from the user: (1) the input TFBS sequences and (2) the length of the flanking sequences. Conclusions: MoRAine 2.0 is an easy-to-use, integrated, and publicly available web tool for the re-annotation of questionable TFBSs. It can be used online or downloaded as a stand-alone version from http://moraine.cebitec.uni-bielefeld.de.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 7(3), 2010

Online-Journal: http://journal.imbio.de/article.php?aid=117
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2010/5016



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