SiteOut: a tool to design motif-free DNA sequences
This tool allows to remove specific nucelotide motifs, such as trancription factor binding sites, from a DNA sequence. It can be used to design a new sequence from scratch, to refine a predefined sequence, or to create neutral spacers between functional sequences. The code will either look for explicit motifs or will use Patser to check for predicted motifs based on the provided frequency matrices (FMs) -collections of FMs ready to be used with SiteOut for D. melanogaster and yeast transcription factors can be downloaded from the links below-. Once you click on 'Submit', your request will be sent to O2, Harvard Medical School's high-perormance computing environment, where it will run for a while. The output will be sent to you by email as soon as it is ready, and will include a .csv file that you can use to visualize the motif content of the sequence with InSite.
A full description of the tool is given in this article, cite it if it was useful for your research!
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