The Hfq-binding small RNAs (sRNAs) have recently drawn much attention as regulators of translation in Escherichia coli. We attempt to identify the targets of this class of sRNAs in genome scale and gain further insight into the complexity of translational regulation induced by Hfq-binding sRNAs. Using it new alignment algorithm, most known negatively regulated targets of Hfq-binding sRNAs were identified. The results also show several interesting aspects of the regulatory function of Hfq-binding sRNAs. (c) 2006 Elsevier Inc. All rights reserved.