Table 2.
Motif Finding Methods
| Software/Method | Input | Summary | Availability | References |
|---|---|---|---|---|
| AMADEUS | DNA or RNA sequences | A method for finding short sequence motifs overrepresented in the promoters or 3′UTRs of a given set of genes | Software package: http://acgt.cs.tau.ac.il/amadeus/download.html | 52 |
| Aptamotif | RNA sequences identified by SELEX | A method for finding sequence-structure motifs in SELEX-derived aptamers. RNA secondary structure is predicted with ensemble-based methods. | Software package: available upon request | 57 |
| CMfinder | RNA sequences | Extension of CM models to search for RNA motifs in a set of unaligned sequences with long flanking regions | Software package and web server: http://bio.cs.washington.edu/yzizhen/CMfinder/ | 58 |
| cERMIT | DNA or RNA sequences and associated expression or affinity measures | A rank-ordered-based method that searches for sequence motifs bested supported by the observed experimental evidence (i.e., semiquantitative genome-wide binding data). It uses the complete dataset and does not require a cutoff to define the positive set. | Software package: http://www.genome.duke.edu/labs/ohler/research/transcription/cERMIT/ | 47 |
| COVE | RNA sequences and alignment (optional) | Implementation of CMs for (1) secondary structure-based multiple sequence alignment; (2) consensus secondary structure prediction; and (iii) secondary structure-based database scanning. | Software package: ftp://selab.janelia.org/pub/software/cove/ | 59 |
| FIRE | DNA or RNA sequences | A method to detect DNA or RNA motifs that model the mutual information between sequences and gene expression measurements. | Software package: http://tavazoielab.princeton.edu/FIRE/ Web server: https://iget.princeton.edu/ |
50 |
| MatrixREDUCE | DNA or RNA sequences and associated expression or affinity measures | A biophysical model to discover sequence-specific binding affinity of the factor of interest (TF or RBP). | Software package: http://bussemaker.bio.columbia.edu/software/MatrixREDUCE/ | 48 |
| MEME | DNA or RNA sequences | A generative model for finding motifs in DNA or protein sequences. Can be used for finding sequence motifs in RNA sequences. | Software package and web server: http://meme.sdsc.edu/meme4_6_0/cgibin/meme.cgi | 49 |
| MEMERIS | RNA sequences and predicted structures | Extension of MEME for finding RNA motifs. It uses RNA structure information as a prior to guide the motif search toward single-stranded regions. | Software package (includes scripts for structure prediction): http://www.bioinf.uni-freiburg.de/∼hiller/MEMERIS/ | 60 |
| REFINE | DNA or RNA sequences | Extension of MEME, filters out regions of target sequences that are relatively devoid of discriminatory hexamers, and then applies MEME motif-finding algorithm. | Software package: http://nar.oxfordjournals.org/content/early/2010/10/18/nar.gkq920/suppl/DC1 | 51 |
| RNAalifold | RNA alignment | A method for detecting conserved RNA secondary structures in a family of related RNA sequences. | Software package: http://www.tbi.univie.ac.at/∼ivo/RNA/ Web server: http://rna.tbi.univie.ac.at/cgibin/RNAalifold.cgi |
61 |
| RNAcontext | RNA sequences, associated affinity measures and predicted structures | A discriminatory approach for finding RNA motifs that represent the sequence and structure preferences of RBPs. RNAcontext can model a wide range of structure features using a flexible alphabet. | Software package (includes scripts for structure prediction): http://morrislab.med.utoronto.ca/software.html | 53 |
| RNApromo | RNA sequences | CM-based model for finding RNA motifs. | Software package and web server: http://genie.weizmann.ac.il/pubs/rnamotifs08/rnamotifs08_predict.html | 62 |