Editing Sequence motif (section)

====''De novo'' motif discovery====
There are software programs which, given multiple input sequences, attempt to identify one or more candidate motifs. One example is the [[Multiple EM for Motif Elicitation]] (MEME) algorithm, which generates statistical information for each candidate.<ref name="Bailey2006">{{cite journal | vauthors = Bailey TL, Williams N, Misleh C, Li WW | title = MEME: discovering and analyzing DNA and protein sequence motifs | journal = Nucleic Acids Research | volume = 34 | issue = Web Server issue | pages = W369-73 | date = July 2006 | pmid = 16845028 | pmc = 1538909 | doi = 10.1093/nar/gkl198 }}</ref> There are more than 100 publications detailing motif discovery algorithms; Weirauch ''et al''. evaluated many related algorithms in a 2013 benchmark.<ref name="Weirauch2013">{{cite journal | vauthors = Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR | display-authors = 6 | title = Evaluation of methods for modeling transcription factor sequence specificity | journal = Nature Biotechnology | volume = 31 | issue = 2 | pages = 126–34 | date = February 2013 | pmid = 23354101 | pmc = 3687085 | doi = 10.1038/nbt.2486 }}
</ref> The [[planted motif search]] is another motif discovery method that is based on combinatorial approach.