SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures

RNA aptamer selection during SELEX experiments builds on secondary structural diversity. Advanced structural comparison methods can focus this diversity. We develop <monospace>SICOR</monospace>, which uses probabilistic subgraph isomorphisms for graph distances between RNA secondary structure graphs. <monospace>SICOR</monospace> outperforms other comparison methods and is applicable to many structural comparisons in experimental design.

[1]  Yann Ponty,et al.  GenRGenS: software for generating random genomic sequences and structures , 2006, Bioinform..

[2]  H. Sommers,et al.  Random bistochastic matrices , 2007, 0711.3345.

[3]  Rolf Backofen,et al.  AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments. , 2016, Cell systems.

[4]  F. Major,et al.  The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data , 2008, Nature.

[5]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[6]  Manuela Helmer-Citterich,et al.  A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications , 2016, Nucleic acids research.

[7]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[8]  Robert Giegerich,et al.  Forest Alignment with Affine Gaps and Anchors , 2011, CPM.

[9]  J. Doye,et al.  Sequence-dependent thermodynamics of a coarse-grained DNA model. , 2012, The Journal of chemical physics.

[10]  Vladimir I. Levenshtein,et al.  On the Minimal Redundancy of Binary Error-Correcting Codes , 1975, Inf. Control..

[11]  Barbara Fink,et al.  Molecular analysis of a synthetic tetracycline-binding riboswitch. , 2005, RNA.

[12]  Namhee Kim,et al.  Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approach. , 2015, Methods in enzymology.

[13]  Martina Rimmele,et al.  Nucleic Acid Aptamers as Tools and Drugs: Recent Developments , 2003, Chembiochem : a European journal of chemical biology.

[14]  Mike A. Steel,et al.  Metrics on RNA Secondary Structures , 2000, J. Comput. Biol..

[15]  Peter C Anderson,et al.  Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state , 2017, PloS one.

[16]  Heinz H. Bauschke,et al.  On Projection Algorithms for Solving Convex Feasibility Problems , 1996, SIAM Rev..

[17]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[18]  Harold W. Kuhn,et al.  The Hungarian method for the assignment problem , 1955, 50 Years of Integer Programming.

[19]  Y. Aflalo,et al.  On convex relaxation of graph isomorphism , 2015, Proceedings of the National Academy of Sciences.

[20]  Gabriele Ausiello,et al.  A novel approach to represent and compare RNA secondary structures , 2014, Nucleic acids research.

[21]  Fei Li,et al.  MicroRNA identification based on sequence and structure alignment , 2005, Bioinform..

[22]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[23]  R. Russell,et al.  The Roles of Chaperones in RNA Folding , 2013 .

[24]  Tamar Schlick,et al.  Graph Applications to RNA Structure and Function , 2013 .

[25]  A. Jäschke,et al.  A small catalytic RNA motif with Diels-Alderase activity. , 1999, Chemistry & biology.

[26]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[27]  J. Collins,et al.  A brief history of synthetic biology , 2014, Nature Reviews Microbiology.

[28]  T. Schlick,et al.  Computational approaches to RNA structure prediction, analysis, and design. , 2011, Current opinion in structural biology.

[29]  Marcel Turcotte,et al.  RiboFSM: Frequent subgraph mining for the discovery of RNA structures and interactions , 2014, BMC Bioinformatics.

[30]  Bin Ma,et al.  A General Edit Distance between RNA Structures , 2002, J. Comput. Biol..

[31]  J. McCaskill.  The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.

[32]  Julien Allali,et al.  Novel Tree Edit Operations for RNA Secondary Structure Comparison , 2004, WABI.

[33]  Namhee Kim,et al.  Network Theory Tools for RNA Modeling. , 2013, WSEAS transactions on mathematics.

[34]  Rolf Backofen,et al.  GraphClust: alignment-free structural clustering of local RNA secondary structures , 2012, Bioinform..

[35]  Joanna Trylska,et al.  Dependency Map of Proteins in the Small Ribosomal Subunit , 2006, PLoS Comput. Biol..

[36]  F. Ducongé,et al.  Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers , 2016, Pharmaceuticals.

[37]  Robert Lee Hotz,et al.  Mathematical and Biological Scientists Assess the State-of-the-Art in RNA Science at an IMA Workshop RNA in Biology, Bioengineering and Biotechnology , 2008 .

[38]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[39]  Kevin P. Murphy,et al.  Efficient parameter estimation for RNA secondary structure prediction , 2007, ISMB/ECCB.

[40]  Thorsten Strufe,et al.  StreAM- T_g : Algorithms for Analyzing Coarse Grained RNA Dynamics Based on Markov Models of Connectivity-Graphs , 2016, WABI.

[41]  Yingfu Li,et al.  Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. , 2004, Chemistry & biology.

[42]  Christus,et al.  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .

[43]  I. Hofacker,et al.  Predicting RNA 3D structure using a coarse-grain helix-centered model , 2015, RNA.

[44]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[45]  M. Yarus,et al.  A More Complex Isoleucine Aptamer with a Cognate Triplet* , 2005, Journal of Biological Chemistry.

[46]  Alan Edelman,et al.  Julia: A Fresh Approach to Numerical Computing , 2014, SIAM Rev..

[47]  Namhee Kim,et al.  RAG: RNA-As-Graphs web resource , 2004, BMC Bioinformatics.

[48]  Alain Denise,et al.  Alignments of RNA Structures , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[49]  Robert Giegerich,et al.  Local similarity in RNA secondary structures , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[50]  R. Knight,et al.  Size, constant sequences, and optimal selection. , 2005, RNA.

[51]  Eun Jeong Cho,et al.  Applications of aptamers as sensors. , 2009, Annual review of analytical chemistry.

[52]  Thorsten Strufe,et al.  StreAM-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$T_g$$\end{document}Tg: algorithms for analyzing coarse grained , 2017, Algorithms for Molecular Biology.