Riboswitches and RNA interference are important emerging mechanisms found in many organisms to control gene expression. To enhance our understanding of such RNA roles, finding small regulatory motifs in genomes presents a challenge on a wide scale. Many simple functional RNA motifs have been found by in vitro selection experiments, which produce synthetic target-binding aptamers as well as cata...

Prediction of protein structural and functional characteristics based on specific motif interactions could serve as a powerful tool in many facets of the biological sciences. Such improvements in protein modeling will be instrumental in the enhancement of drug design. A new approach to a sequence description of EF-hand motifs with more than one EF-hand domain is presented here; this permits pre...

Introduction In biology, sequence motifs are short sequence patterns, usually with fixed lengths, that represent many features of DNA, RNA, and protein molecules. Sequence motifs can represent transcription factor binding sites for DNA, splice junctions for RNA, and binding domains for proteins. Thus, discovering sequence motifs can lead to a better understanding of transcriptional regulation, ...

AUTOMATED DATA-DRIVEN DISCOVERY OF MOTIF-BASED PROTEIN FUNCTION CLASSIFIERS Xiangyun Wang, Diane Schroeder, Drena Dobbs, and Vasant Honavar Artificial Intelligence Laboratory Department of Computer Science and Graduate Program in Bioinformatics and Computational Biology Iowa State University Ames, IA 50011, USA www.cs.iastate.edu/~honavar/aigroup.html [email protected] ABSTRACT This paper ...

ABSTRACT The number of long noncoding RNAs (lncRNAs) with characterized developmental and cellular functions continues to increase, but our understanding the molecular mechanisms underlying lncRNA functions, how they are dictated by RNA sequences, remains limited. Relatively short, conserved sequence motifs embedded in transcripts often important determinants localization, stability interaction...