Volume 703 of the series Methods in Molecular Biology pp 67-86


Web-Based Tools for Studying RNA Structure and Function

  • Ajish D. GeorgeAffiliated withDepartment of Biomedical Sciences, School of Public Health, Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY Email author 
  • , Scott A. TenenbaumAffiliated withCollege of Nanoscale Science and Engineering, Nanoscale Constellation, University at Albany-SUNY

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Like protein coding sequences, functional motifs in RNA elements are frequently conserved, but this conservation is most often at the structure level rather than sequence based. Proper characterization of these structural RNA motifs is both the key and the limiting step to understanding the nature of RNA–protein interactions. The discovery of elements targeted by RNA-binding proteins and how they function remains one of the most active, yet elusive areas of RNA biology. Only a limited number of these elements have been well characterized with many of the fundamental rules yet to be discovered. Here we present a comprehensive list of web based resources that can be used in the study and identification of RNA-based structural and regulatory motifs and provide a survey of the informatic resources that can have been developed to facilitate this research.

Key words

RNA RNA-binding Protein (RBP) RNA motifs RNA binding sites