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PPP
perform promoter prediction on FASTA formatted DNA sequences

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by Aldert L. Zomer

Predicts promoter sequences and transcription factor binding sites using a HMM model with hmmer.

If you make use of PPP for your research, please use for the SigmaA binding site models the following text: Upstream regions were scanned for putative (Lactococcal-like) SigmaA binding sites using PPP (http://bioinformatics.biol.rug.nl/websoftware/ppp). Hidden Markov models of the lactococcal Sigma A binding site, allowing 15 to 19 bp of space between the canonical -35 and -10 promoter elements were constructed using alignments of known Sigma A binding sites. More details can be found in Zomer AL, Buist G, Larsen R, Kok J, Kuipers OP, Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363, J Bacteriol. 2007, 189:1366-81.


Data Submission Form

Your data will be processed on the MolGen linux server and the results will be made available on the results page which can be bookmarked.
The data will be stored on our server for up to three weeks and will be kept confidential.

promoter prediction needs a fasta formatted file of your upstream region(s)(example).
Select FASTA formatted DNA sequences to upload


Or paste your sequences here


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