ChIPMunk v4.3+ released [May 20, 2013] http://autosome.ru/ChIPMunk
ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping.
ChIPMunk identifies the strong motif with the maximum Discrete Information Content in a set of DNA sequences,
Quick-start guide: pdf,pptx.
ChIPMunk v4 (check the downloads section) uses extended multifasta as the input format and supports IUPAC DNA letters in the input sequences. ChIPHorde extension can be used to discover different motifs in a given dataset. ChIPMunk is now able to use the motif shape priors, see details in the manual. Since v3 ChIPMunk can be easily integrated with other Java-based software.
Web-version (v3.2a). Input is limited to a 200kb total data size.
Citation Kulakovskiy IV, Boeva VA, Favorov AV, Makeev VJ
The work was supported by Russian Fund of Basic Research projects [07-04-01623 and 07-04-01584]; INTAS Project [05-1000008-8028]; Russian Federation Agency in Science and Innovation State Contract [02.531.11.9003, 02.740.11.5008]; Russian Academy of Sciences Program in Molecular and Cellular Biology, Project #10; and French INRIA Équipe associé MIGEC. This work was also supported, in part, by a Dynasty Foundation Fellowship to I.V.K.