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MotifViz - Integration of tools for detecting overrepresented motifs

We present 4 different Cis-element search programs for identifying functional sites in DNA sequences. Given a set of DNA sequences that share a common function, these programs can compare them to a library of sequence motifs (e.g. transcription factor binding patterns), and identify which if any of the motifs are statistically overrepresented in the sequence set:

  • Possum: simple PWM(Position-specific Weight Matrix) scan, fast but without statistical evaluation.
  • Motifish: use PWM scan and Fisher Exact Test to compare the number sequences a motif occurs in query sequence set vs background set.
  • Rover: use PWM scan and binomial estimation to compare the number of motif occurrences in query sequences vs background.
  • Clover: use a thermodynamic model with permutation or background input for statistical evaluation of Cis-eLement OVERrepresentation, more sophisticated but slow compared to the other 3 programs.

References to these programs can be found in: 1. Frith, M. C., Fu,Y., Yu, L., Chen, J. F., Hansen, U. & Weng, Z. (2004) Detection of Functional DNA Motifs via Statistical Overrepresentation. Nucleic Acids Research (In Print) 2. Haverty, P. M., Hansen, U. & Weng, Z. (2004) Computational Inference of Transcriptional Regulatory Networks from Expression Profiling and Transcription Factor Binding Site Identification. Nucleic Acids Res. 2004 Jan 1;32(1):179-188.

Protein Engineering