MDScan (Motif Discovery scan) discovers conserved transcription factor binding sites among upstream sequences from chromatin immune precipitation experiments (CHIP) as well as from single microarray experiments. The algorithm is strictly deterministic, not discovering local minima and always giving the globally best conserved motif. It is faster than most other algorithms and nearly as sensitive as BioProspector.
- windows with Cygwin / Linux / Mac OsX
- C Complier
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Liu XS, Brutlag DL, Liu JS.
An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments.
Nat Biotechnol. 2002 20(8):835-9.