==See also==*Biomolecular structure*Multiple EM for Motif Elicitation*Nucleic acid sequence*Protein primary structure*Sequence logo*Sequence mining*Structural motif*Short linear motif==References====Further reading====External links=====Motif-finding methods and databases===* EXTREME — An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data* kmerHMM: a Hidden Markov Model method for motif discovery on protein binding microarray data* PMS or [http://motifsearch.com] — for discovery of de novo DNA/Protein motifs (from University of Connecticut)* Amadeus and Allegro motif finding platforms (from Tel-Aviv University)* PROSITE — database of protein families and domains* Database and Analysis Suite for Quadruplex forming motifs in Nucleotide Sequences* MEME Suite of motif-based sequence analysis tools* TRANSFAC — a commercial (limited public access) database for transcription factor motifs* eMotif (from Stanford University)* HOCOMOCO — "Homo sapiens" Comprehensive Model Collection of transcription factor binding models obtained by careful integration of data from different sources* Bioprospector (from Stanford University)* Cis-analysis — list of and comments on other programs useful for discovering cis-regulatory element motifs* NCBI Home Page — NIH's National Library of Medicine NCBI (National Center for Biotechnology Information) link to a tremendous number of resources including sequence analysis and motif discovery.
* kmerHMM: a Hidden Markov Model method for motif discovery on protein binding microarray data* PMS or [http://motifsearch.com] — for discovery of de novo DNA/Protein motifs (from University of Connecticut)* Minimotif Miner — for discovery of short contiguous motifs of known function (from University of Nevada Las Vegas and University of Connecticut)* Amadeus and Allegro motif finding platforms (from Tel-Aviv University)* PROSITE — database of protein families and domains* Database and Analysis Suite for Quadruplex forming motifs in Nucleotide Sequences* MEME Suite of motif-based sequence analysis tools* TRANSFAC — a commercial (limited public access) database for transcription factor motifs* eMotif (from Stanford University)* HOCOMOCO — Homo Sapiens Comprehensive Model Collection of transcription factor binding models obtained by careful integration of data from different sources* Bioprospector (from Stanford University)* FIRE motif discovery approach (from the Tavazoie lab at Princeton)* Cis-analysis — list of and comments on other programs useful for discovering cis-regulatory element motifs* NCBI Home Page — NIH’s National Library of Medicine NCBI (National Center for Biotechnology Information) link to a tremendous number of resources including sequence analysis and motif discovery.