This web page was produced as an assignment for Gen677, an undergraduate course at UW-Madison Spring 2009
DNA Motifs
I first tried to use MOTIF to find DNA motifs, which limited me to only using 60,000 of the over 170,000 bases in human SORL1. However, no matter what I used for settings, I was unable to find any motifs. Using MEME on the other hand resulted in three DNA motifs. Again, I was limited to using 60,000 bases. The motif above is an example of the MEME output. The larger a letter is, the more certain that base is in that position. In this case, the full-sized letters are non-variable. Because of the limitation on the number of bases used, it is hard to determine how many DNA motifs occur and how frequently they appear.
References
Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
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Last Updated 5/13/09
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