StemSearch: RNA search tool based on stem identification and indexing.
暂无分享,去创建一个
[1] Michael Zuker,et al. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..
[2] D. Sankoff. Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems , 1985 .
[3] D. Turner,et al. Improved free-energy parameters for predictions of RNA duplex stability. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[4] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[5] J. McCaskill. The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.
[6] R. Durbin,et al. RNA sequence analysis using covariance models. , 1994, Nucleic acids research.
[7] D. Turner,et al. Predicting oligonucleotide affinity to nucleic acid targets. , 1999, RNA.
[8] S. Eddy. Non–coding RNA genes and the modern RNA world , 2001, Nature Reviews Genetics.
[9] D. Ecker,et al. RNAMotif, an RNA secondary structure definition and search algorithm. , 2001, Nucleic acids research.
[10] Ali Nahvi,et al. Genetic control by a metabolite binding mRNA. , 2002, Chemistry & biology.
[11] Sean R. Eddy,et al. RSEARCH: Finding homologs of single structured RNA sequences , 2003, BMC Bioinformatics.
[12] Ivo L. Hofacker,et al. Vienna RNA secondary structure server , 2003, Nucleic Acids Res..
[13] Terrence S. Furey,et al. The UCSC Genome Browser Database , 2003, Nucleic Acids Res..
[14] Sam Griffiths-Jones,et al. The microRNA Registry , 2004, Nucleic Acids Res..
[15] Stéphane Vialette,et al. On the computational complexity of 2-interval pattern matching problems , 2004, Theor. Comput. Sci..
[16] G. Stormo,et al. A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. , 2004, Bioinformatics.
[17] David B. Allison,et al. Chebyshev's inequality for nonparametric testing with small N and α in microarray research , 2004 .
[18] István Miklós,et al. Co-transcriptional folding is encoded within RNA genes , 2004, BMC Molecular Biology.
[19] B. Haas,et al. Searching Genomes for Noncoding RNA Using FastR , 2005, TCBB.
[20] Jan Krüger,et al. RNAhybrid: microRNA target prediction easy, fast and flexible , 2006, Nucleic Acids Res..
[21] Roded Sharan,et al. A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements , 2006, ISMB.
[22] Serafim Batzoglou,et al. CONTRAfold: RNA secondary structure prediction without physics-based models , 2006, ISMB.
[23] Zasha Weinberg,et al. CMfinder - a covariance model based RNA motif finding algorithm , 2006, Bioinform..
[24] Rolf Backofen,et al. Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering , 2007, PLoS Comput. Biol..
[25] Hervé Isambert,et al. The jerky and knotty dynamics of RNA. , 2009, Methods.
[26] Yann Ponty,et al. VARNA: Interactive drawing and editing of the RNA secondary structure , 2009, Bioinform..
[27] Satish Chikkagoudar,et al. PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences , 2010, Nucleic Acids Res..
[28] Michael Beckstette,et al. Structator: fast index-based search for RNA sequence-structure patterns , 2011, BMC Bioinformatics.
[29] Wojciech Rytter,et al. Extracting Powers and Periods in a String from Its Runs Structure , 2010, SPIRE.
[30] Matthias Zytnicki,et al. BlastR—fast and accurate database searches for non-coding RNAs , 2011, Nucleic acids research.
[31] A. Chinnaiyan,et al. The emergence of lncRNAs in cancer biology. , 2011, Cancer discovery.
[32] L. Maquat,et al. lncRNAs transactivate Staufen1-mediated mRNA decay by duplexing with 3'UTRs via Alu elements , 2010, Nature.
[33] James B. Brown,et al. Long noncoding RNAs are rarely translated in two human cell lines , 2012, Genome research.
[34] Michael Beckstette,et al. Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns , 2013, BMC Bioinformatics.
[35] Rolf Backofen,et al. LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search , 2013, Algorithms for Molecular Biology.