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Published online 1 April 2004

Nucleic Acids Research, 2004, Vol. 32, No. 6 1973-1981

Transcriptional organization of the Clostridium acetobutylicum genome

Carlos J. Paredes, Isidore Rigoutsos1,2 and E. Terry Papoutsakis*,1

Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA, 1 Bioinformatics and Pattern Discovery Group, IBM TJ Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA and 2 Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA

*To whom correspondence should be addressed. Tel: +1 847 491 7455; Fax: +1 847 4913728; Email: e-paps{at}northwestern.edu

Received December 24, 2003; Revised and Accepted March 8, 2004

Prokaryotic genes are frequently organized in multicistronic operons (or transcriptional units, TUs), and usually the regulatory motifs for the whole TU are located upstream of the first TU gene. Although the number of sequenced genomes has increased dramatically, experimental information on TU organization is extremely limited. Even for organisms as extensively studied as Escherichia coli and Bacillus subtilis, TU annotation is far from complete. It therefore becomes imperative to rely on computational approaches to complement experimental information. Here we present a TU map for the obligate anaerobe Clostridium acetobutylicum ATCC 824. This map is largely based on the distance between pairs of consecutive genes but enhanced and refined by predictions of several types of promoters ({sigma}A, {sigma}E and {sigma}F/G) and rho-independent terminator structures. Based on the set of known C.acetobutylicum TUs, the presented TU map offers an 88% prediction accuracy.


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