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Informatic Resources for Identifying and Annotating Structural RNA Motifs

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Abstract

Post-transcriptional regulation of genes and transcripts is a vital aspect of cellular processes, and unlike transcriptional regulation, remains a largely unexplored domain. One of the most obvious and most important questions to explore is the discovery of functional RNA elements. Many RNA elements have been characterized to date ranging from cis-regulatory motifs within mRNAs to large families of non-coding RNAs. Like protein coding genes, the functional motifs of these RNA elements are highly conserved, but unlike protein coding genes, it is most often the structure and not the sequence that is conserved. Proper characterization of these structural RNA motifs is both the key and the limiting step to understanding the post-transcriptional aspects of the genomic world. Here, we focus on the task of structural motif discovery and provide a survey of the informatics resources geared towards this task.

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Acknowledgments

We wish to thank the members of the Tenenbaum Lab for helpful suggestions and discusion, especially Chris Zaleski and Frank Doyle. This work was supported in part by NIH grant U01HG004571 to SAT from the NHGRI.

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  1. Gen*NY*Sis Center for Excellence in Cancer Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany-SUNY, 1 Discovery Drive, Room 220, Rensselaer, NY, 12144, USA

    Ajish D. George & Scott A. Tenenbaum

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George, A.D., Tenenbaum, S.A. Informatic Resources for Identifying and Annotating Structural RNA Motifs. Mol Biotechnol 41, 180–193 (2009). https://doi.org/10.1007/s12033-008-9114-z

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