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PePPER: a webserver for prediction of prokaryote promoter elements and regulons

Anne de Jong123, Hilco Pietersma123, Martijn Cordes123, Oscar P Kuipers123 and Jan Kok12*

Author Affiliations

1 Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, 9747 AG, Groningen, The Netherlands

2 Top Institute Food and Nutrition, Wageningen, The Netherlands

3 The Netherlands Kluyver Centre for Genomics of Industrial Fermentations, Delft, The Netherlands/Netherlands Consortium of Systems Biology, Amsterdam, The Netherlands

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BMC Genomics 2012, 13:299  doi:10.1186/1471-2164-13-299

Published: 2 July 2012

Additional files

Additional file 1 Table S1:

Lactococcus lactis TFBS WebLogos. Column 1 presents all known (studied) regulons of L. lactis. Alternative names for TFBS are given in column 2. The consensus sequence given in columns 3 were taken from the literature references from Table 1. In column 4, the TFBS identities are given that are used by PePPER. The upstream sequences of the genes of the regulons indicated in column 1 were aligned using MEME [9]. The obtained DNA motifs (WebLogos) are presented in column 5.

Format: PPTX Size: 319KB Download file

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