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22
Partition function and base pairing probabilities of RNA heterodimers
- Algorithms Mol Biol
, 2006
"... Abstract Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, noncoding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inte ..."
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Cited by 65 (14 self)
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Abstract Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, noncoding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods: The standard dynamic programming algorithms for computing secondary structures of linear singlestranded RNA molecules are extended to the co-folding of two interacting RNAs. Results: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.
The expansion of the metazoan microRNA repertoire
- The Students of Bioinformatics Computer Labs 2004 and 2005
, 2006
"... MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at ..."
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Cited by 45 (3 self)
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MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at least one species. Using this uniform data basis we analyze their evolutionary history in terms of individual gene phylogenies and in terms of preservation of genomic nearness across species. This allows us to reliably identify microRNA clusters that are derived from a common transcript. We identify three episodes of microRNA innovation that correspond to major developmental innovations: A class of about 20 miRNAs is common to protostomes and deuterostomes and might be related to the advent of bilaterians. A second large wave of innovations maps to the branch leading to the vertebrates. The third significant outburst of miRNA innovation coincides with placental (eutherian) mammals. In addition, we observe the expected expansion of the microRNA inventory due to genome duplications in early vertebrates and in an ancestral teleost. The non-local duplications in the vertebrate ancestor are predated by local (tandem) duplications leading to the formation of about a dozend ancient microRNA clusters.
ptRNApred: computational identification and classification of post-transcriptional RNA
, 2013
"... Non-coding RNAs (ncRNAs) are known to play im-portant functional roles in the cell. However, their identification and recognition in genomic sequences remains challenging. In silico methods, such as clas-sification tools, offer a fast and reliable way for such screening and multiple classifiers have ..."
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Cited by 1 (0 self)
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Non-coding RNAs (ncRNAs) are known to play im-portant functional roles in the cell. However, their identification and recognition in genomic sequences remains challenging. In silico methods, such as clas-sification tools, offer a fast and reliable way for such screening and multiple classifiers have already been developed to predict well-defined subfamilies of RNA. So far, however, out of all the ncRNAs, only tRNA, miRNA and snoRNA can be predicted with a satisfying sensitivity and specificity. We here present ptRNApred, a tool to detect and classify subclasses of non-coding RNA that are involved in the regu-lation of post-transcriptional modifications or DNA replication, which we here call post-transcriptional RNA (ptRNA). It (i) detects RNA sequences cod-ing for post-transcriptional RNA from the genomic sequence with an overall sensitivity of 91 % and a specificity of 94 % and (ii) predicts ptRNA-subclasses that exist in eukaryotes: snRNA, snoRNA, RNase P, RNase MRP, Y RNA or telomerase RNA. AVAILABIL-ITY: The ptRNApred software is open for public use on
unknown title
, 2007
"... thermodynamically stable and evolutionarily conserved RNA structures ..."
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unknown title
, 2007
"... The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures ..."
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The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures
Variations on RNA folding -- Locally stable structures . . .
, 2007
"... In recent years, the importance of RNA molecules in living cells has been recognized, and consequently the interest in RNA related science has increased dramatically. We introduce here new computational tools as well as modifications to established tools for thermodynamic RNA secondary structure pre ..."
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In recent years, the importance of RNA molecules in living cells has been recognized, and consequently the interest in RNA related science has increased dramatically. We introduce here new computational tools as well as modifications to established tools for thermodynamic RNA secondary structure prediction. These tools cover a variety of problems: • Prediction of local RNA structures • Prediction of RNA-RNA hybridization structures • Extension of consensus structure prediction of RNA alignments • Extension of RNA single structure prediction • Prediction of local consensus structures of RNA alignments The tools RNAcofold and RNAplfold cover the partition function and pair probability of the structure of RNA dimers as well as local partition functions and pair probability, respectively. RNAcofold can also predict equilibrium concentrations of dimers and monomers dependent on given initial concentrations of monomers. The existing algorithm RNAfold has been modified to include the partition function of canonical structures and a faster com-putation of interior-loop energy. The energy evaluation of the consensus structure prediction tool RNAalifold has been changed to a more realistic physical model. Furthermore, the possibility of sequence weighting has been added toRNAalifold, and a local version, RNALalifold, has been developed. We show some applications of these new programs, which range from analysis of siRNA/mRNA interaction for RNAcofold and accessibility prediction of RNA interaction target sites for RNAplfold. We can, using other groups’ experimental results, conclude that the reported lack of miRNA function when too many GU base pairs are present may be due to a change in the binding at i the 5’ region of the miRNA. We also show that the new RNAalifold program outperforms the previous version at least when the alignments contain many gaps. The programs developed are part of the freely available ViennaRNA software package, and can be downloaded from
Nucleic Acids Research, 2009, 1–14 doi:10.1093/nar/gkn1084
, 2008
"... Non-coding RNA annotation of the genome ..."
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doi:10.1093/nar/gkn1084 Non-coding RNA annotation of the genome of Trichoplax adhaerens
, 2008
"... A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast iden ..."
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A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs—in particular rRNAs, tRNAs and some snRNAs—we developed a semiglobal dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as singlecopy genes or with very small copy numbers in the Trichoplax genome.
CHAPTER 1
"... The advent of high-throughput techniques that allow comprehensive unbiased studies of transcription has lead to a dramatic change in our understanding of genome organization. A decade ago, the genome was seen as a linear arrangement of separated individual genes which are predominantly protein-codin ..."
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The advent of high-throughput techniques that allow comprehensive unbiased studies of transcription has lead to a dramatic change in our understanding of genome organization. A decade ago, the genome was seen as a linear arrangement of separated individual genes which are predominantly protein-coding, with a small set of ancient non-coding “housekeeping”
unknown title
"... MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at ..."
Abstract
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MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at least one species. Using this uniform data basis we analyze their evolutionary history in terms of individual gene phylogenies and in terms of preservation of genomic nearness across species. This allows us to reliably identify microRNA clusters that are derived from a common transcript.
