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Bioinformatics Vol. 18 no. 2 2002
Pages 331-332
© 2002 Oxford University Press

Applications Note

INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling

Gert Thijs 1, Yves Moreau 1, Frank De Smet 1, Janick Mathys 1, Magali Lescot 1, Stephane Rombauts 2, Pierre Rouze 3, Bart De Moor 1 and Kathleen Marchal 1,*

1 ESAT_ SISTA/COSIC, KULeuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium
2 Department of Plant Genetics
3 INRA Associated Laboratory, VIB, UGent, Ledeganckstraat 35, 9000 Gent, Belgium

Received on June 20, 2001 ; revised on August 20, 2001 ; accepted on September 20, 2001

Summary: INCLUSive allows automatic multistep analysis of microarray data (clustering and motif finding). The clustering algorithm (adaptive quality-based clustering) groups together genes with highly similar expression profiles. The upstream sequences of the genes belonging to a cluster are automatically retrieved from GenBank and can be fed directly into Motif Sampler, a Gibbs sampling algorithm that retrieves statistically over-represented motifs in sets of sequences, in this case upstream regions of co-expressed genes.

Availability: For academic purposes at http://www.esat.kuleuven.ac.be/~dna/BioI/Software.html

Contact: Gert.Thijs{at}esat.kuleuven.ac.be

* To whom correspondence should be addressed. Email: Kathleen.Marchal{at}esat.kuleuven.ac.be.


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