WebMOTIFS searches for motifs (repeated elements) in DNA sequences, specified by a list of genes or probes provided by the user. WebMOTIFS retrieves the corresponding sequences, which are automatically passed to the requested motif discovery programs.
WebMOTIFS currently supports motif discovery for DNA from S. cerevisiae, M. musculus, and H. sapiens.
WebMOTIFS can analyze either promoter regions or ChIP-chip data.
How sequences are retrieved: For analysis of promoter regions, WebMOTIFS retrieves a user-specified region (for example, from -500 to +200 bp) around the transcription start site for every gene specified.
For analysis of ChIP-chip data, WebMOTIFS retrieves a sequence window centered around the specified probe. For PCR-based arrays, the sequence windows consist of the entire probe sequence (and often some additional base pairs upstream and downstream of the probe). For oligonucleotide arrays, the sequence windows are centered on the probe sequence, with several hundred base pairs retrieved upstream and downstream of the probe. The sizes of the sequence windows retrieved for each array are listed here, along with other details about ChIP-chip array platforms.
WebMOTIFS avoids retrieving overlapping sequences. Thus, if the user enters a series of closely spaced probes (such that the sequence windows corresponding to the probes overlap), WebMOTIFS will retrieve a sequence corresponding to the entire bound region.
WebMOTIFS submits these sequences to individual motif discovery programs without further processing. In particular, repeats and coding exons are not masked. Individual motif discovery programs may therefore report simple repeats in their results, but these results are largely eliminated during postprocessing.
Format for input: Users can either paste a list of gene/probe names into a text box or upload a text file with a list of names. Names should be entered one per line. If you upload a file of names, it must be saved as plain text. (Other formats, such as *.rtf and *.doc, will make WebMOTIFS unable to recognize your gene/probe names.)
Currently, the hypotheses offered by WebMOTIFS are the Family Binding Profiles(FBPs) compiled by Macisaac et al. Family Binding Profiles summarize the binding specificities of the most common DNA-binding domains. A list of the family binding profiles is available here.
If you know the DNA binding domain of your transcription factor of interest, you may select the corresponding FBP as an initial hypothesis. If you know nothing about the structure of your transcription factor of interest, you can run Bayesian motif discovery using all of the FBPs as possible initial hypotheses.
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