RAG: RNA-As-Graphs web resource

BMC Bioinformatics
Daniela FeraTamar Schlick

Abstract

The proliferation of structural and functional studies of RNA has revealed an increasing range of RNA's structural repertoire. Toward the objective of systematic cataloguing of RNA's structural repertoire, we have recently described the basis of a graphical approach for organizing RNA secondary structures, including existing and hypothetical motifs. We now present an RNA motif database based on graph theory, termed RAG for RNA-As-Graphs, to catalogue and rank all theoretically possible, including existing, candidate and hypothetical, RNA secondary motifs. The candidate motifs are predicted using a clustering algorithm that classifies RNA graphs into RNA-like and non-RNA groups. All RNA motifs are filed according to their graph vertex number (RNA length) and ranked by topological complexity. RAG's quantitative cataloguing allows facile retrieval of all classes of RNA secondary motifs, assists identification of structural and functional properties of user-supplied RNA sequences, and helps stimulate the search for novel RNAs based on predicted candidate motifs.

References

Dec 11, 1999·Nucleic Acids Research·F H van BatenburgJ Oliehoek
Jun 29, 2000·Annual Review of Biochemistry·D S Wilson, J W Szostak
Dec 6, 2001·Nature Reviews. Genetics·S R Eddy
Dec 26, 2001·Nucleic Acids Research·Uma NagaswamyGeorge E Fox
May 23, 2002·Science·Gisela Storz
May 31, 2002·Acta Crystallographica. Section D, Biological Crystallography·Helen M BermanChristine Zardecki
Jan 10, 2003·Nucleic Acids Research·Sam Griffiths-JonesSean R Eddy
Jun 26, 2003·Nucleic Acids Research·Ivo L Hofacker
Dec 19, 2003·Nucleic Acids Research·Makio TamuraStephen R Holbrook
Feb 14, 2004·Bioinformatics·Hin Hark GanTamar Schlick
Apr 21, 2004·Journal of Molecular Biology·Mirela AndronescuAnne Condon
Aug 24, 2004·Journal of Molecular Biology·Namhee KimTamar Schlick

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Citations

Apr 3, 2009·Nucleic Acids Research·Liam ChildsDirk Walther
Oct 22, 2010·BMC Bioinformatics·Denise R KoesslerTeresa Haynes
Jun 2, 2011·BMC Bioinformatics·Joseph A IzzoTamar Schlick
Oct 21, 2005·BMC Bioinformatics·Joshua J FormanStephen J Haggarty
Apr 12, 2008·BMC Bioinformatics·Wenjie ShuShengqi Wang
Jan 6, 2009·BMC Bioinformatics·Darby Tien-Hao ChangJian-Wei Chen
Dec 23, 2011·RNA·Ajaykumar GopalWilliam M Gelbart
Apr 9, 2011·Genetics and Molecular Research : GMR·K Han
Apr 15, 2011·Genetics and Molecular Research : GMR·P XuanY Liu
Aug 26, 2015·Nucleic Acids Research·Mai ZahranTamar Schlick
May 6, 2017·Bioinformatics·Nicolò Navarin, Fabrizio Costa
Jun 27, 2017·Biophysical Journal·Liuba MazzantiSamuela Pasquali
Oct 19, 2016·PloS One·Jiajie HuangMichael Gribskov
Aug 24, 2018·Nucleic Acids Research·Swati JainTamar Schlick
Jan 20, 2020·Biochimica Et Biophysica Acta. General Subjects·Swati JainTamar Schlick
May 10, 2018·Biophysical Journal·Chi H Mak, Ethan N H Phan
Apr 23, 2021·Biophysical Journal·Chi H Mak, Ethan N H Phan
Mar 9, 2010·New Biotechnology·Benoît MasquidaFabrice Jossinet
Apr 26, 2011·Current Opinion in Structural Biology·Christian Laing, Tamar Schlick

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Software Mentioned

- As - Graphs ( RAG )
RNA Matrix Program
RNA
Matrix
Vienna RNAfold
RAG
Mfold
PAM
RNA Matrix

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