Copyright 2004-2007, Trustees of Dartmouth College

Permission is granted to reproduce and use this program for non-profit educational purposes. Commercial licensing is also available. Requests to reproduce or use this program for other than non-profit educational purposes should be addressed to: robert.h.gross@dartmouth.edu

Please cite your use of this code as follows:

• For the BEAM algorithm (non-degenerate motifs of arbitrary length): Carlson* JM, Chakravarty* A, and Gross RH. "BEAM: A beam search algorithm for the identification of cis-regulatory elements in groups of genes." Journal of Computational Biology, 2006; 13(3):686-701.
• For use of PRISM (degenerate motifs from non-degenerate motifs. Implemented in the LO method of edu.dartmouth.bglab.beam.Ambiguizer.java, Carson* JM, Chakravarty* A, Khetani RS, and Gross RH. "Bounded search for de novo identification of degenerate cis-regulatory elements." BMC Bioinformatics, 2006 May 15; 7(1):254.
• For use of SPACER (bipartite motifs): Chakravarty A, Carlson JM, , Khetani RS, DeZiel CE, and Gross RH. "SPACER: Robust identification of cis-regulatory elements with non-contiguous critical residues." Bioinformatics 23: 1029-1031 (2007).
• For use of SCOPE (ensemble method that combines these three algorithms): Chakravarty, A, Carlson, JM, Khetani, RS, and Gross, RH, "A parameter-free algorithm for improved de novo identification of transcription factor binding sites." BMC Bioinformatics, in press (2007).

If you find this program or the source code useful, please let us know. Also, please report bugs to robert.h.gross@dartmouth.edu