Maximum expected accuracy structural neighbors of an RNA secondary structure.

Abstract:

BACKGROUND:Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detect general (i.e., not family specific) entire riboswitches (both aptamer and expression platform) with accuracy. Thus, the development of additional algorithms to detect conformational switches seems important, especially since the difference in free energy between the two metastable secondary structures may be as large as 15-20 kcal/mol. It has recently emerged that RNA secondary structure can be more accurately predicted by computing the maximum expected accuracy (MEA) structure, rather than the minimum free energy (MFE) structure. RESULTS:Given an arbitrary RNA secondary structure S₀ for an RNA nucleotide sequence a = a₁,..., a(n), we say that another secondary structure S of a is a k-neighbor of S₀, if the base pair distance between S₀ and S is k. In this paper, we prove that the Boltzmann probability of all k-neighbors of the minimum free energy structure S₀ can be approximated with accuracy ε and confidence 1 - p, simultaneously for all 0 ≤ k < K, by a relative frequency count over N sampled structures, provided that N>N(ε,p,K)=Φ⁻¹(p/2K)²/4ε², where Φ(z) is the cumulative distribution function (CDF) for the standard normal distribution. We go on to describe the algorithm RNAborMEA, which for an arbitrary initial structure S₀ and for all values 0 ≤ k < K, computes the secondary structure MEA(k), having maximum expected accuracy over all k-neighbors of S₀. Computation time is O(n³ · K²), and memory requirements are O(n² · K). We analyze a sample TPP riboswitch, and apply our algorithm to the class of purine riboswitches. CONCLUSIONS:The approximation of RNAbor by sampling, with rigorous bound on accuracy, together with the computation of maximum expected accuracy k-neighbors by RNAborMEA, provide additional tools toward conformational switch detection. Results from RNAborMEA are quite distinct from other tools, such as RNAbor, RNAshapes and paRNAss, hence may provide orthogonal information when looking for suboptimal structures or conformational switches. Source code for RNAborMEA can be downloaded from http://sourceforge.net/projects/rnabormea/ or http://bioinformatics.bc.edu/clotelab/RNAborMEA/.

journal_name

BMC Bioinformatics

journal_title

BMC bioinformatics

authors

Clote P,Lou F,Lorenz WA

doi

10.1186/1471-2105-13-S5-S6

subject

Has Abstract

pub_date

2012-04-12 00:00:00

pages

S6

issn

1471-2105

pii

1471-2105-13-S5-S6

journal_volume

13 Suppl 5

pub_type

杂志文章
  • EVEREST: automatic identification and classification of protein domains in all protein sequences.

    abstract:BACKGROUND:Proteins are comprised of one or several building blocks, known as domains. Such domains can be classified into families according to their evolutionary origin. Whereas sequencing technologies have advanced immensely in recent years, there are no matching computational methodologies for large-scale determina...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-277

    authors: Portugaly E,Harel A,Linial N,Linial M

    更新日期:2006-06-02 00:00:00

  • A semi-parametric statistical model for integrating gene expression profiles across different platforms.

    abstract:BACKGROUND:Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene expression levels. However, considerable discrepancy has been found between DEGs detected using the t...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0847-y

    authors: Lyu Y,Li Q

    更新日期:2016-01-11 00:00:00

  • Repliscan: a tool for classifying replication timing regions.

    abstract:BACKGROUND:Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replica...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-017-1774-x

    authors: Zynda GJ,Song J,Concia L,Wear EE,Hanley-Bowdoin L,Thompson WF,Vaughn MW

    更新日期:2017-08-07 00:00:00

  • An SVM-based method for assessment of transcription factor-DNA complex models.

    abstract:BACKGROUND:Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex structures, protein-DNA docking can be used to predict native or near-native...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-018-2538-y

    authors: Corona RI,Sudarshan S,Aluru S,Guo JT

    更新日期:2018-12-21 00:00:00

  • BIOSMILE: a semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features.

    abstract:BACKGROUND:Bioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information extraction (IE) systems that incorporate natural language processing (NLP) techniques have thus been developed for use in the biomedical fi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-325

    authors: Tsai RT,Chou WC,Su YS,Lin YC,Sung CL,Dai HJ,Yeh IT,Ku W,Sung TY,Hsu WL

    更新日期:2007-09-01 00:00:00

  • Multiple virtual screening approaches for finding new hepatitis C virus RNA-dependent RNA polymerase inhibitors: structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors.

    abstract::The RNA polymerase NS5B of Hepatitis C virus (HCV) is a well-characterised drug target with an active site and four allosteric binding sites. This work presents a workflow for virtual screening and its application to Drug Bank screening targeting the Hepatitis C Virus (HCV) RNA polymerase non-nucleoside binding sites....

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-13-S17-S5

    authors: Elhefnawi M,ElGamacy M,Fares M

    更新日期:2012-01-01 00:00:00

  • ImiRP: a computational approach to microRNA target site mutation.

    abstract:BACKGROUND:MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6-8 nucleotide long target sites, usually located within the mRNA 3' untranslated region. A common approach to validate and probe microRNA-mRNA interact...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-016-1057-y

    authors: Ryan BC,Werner TS,Howard PL,Chow RL

    更新日期:2016-04-27 00:00:00

  • Pripper: prediction of caspase cleavage sites from whole proteomes.

    abstract:BACKGROUND:Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to pre...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-320

    authors: Piippo M,Lietzén N,Nevalainen OS,Salmi J,Nyman TA

    更新日期:2010-06-15 00:00:00

  • tcR: an R package for T cell receptor repertoire advanced data analysis.

    abstract:BACKGROUND:The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is req...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0613-1

    authors: Nazarov VI,Pogorelyy MV,Komech EA,Zvyagin IV,Bolotin DA,Shugay M,Chudakov DM,Lebedev YB,Mamedov IZ

    更新日期:2015-05-28 00:00:00

  • TreeDyn: towards dynamic graphics and annotations for analyses of trees.

    abstract:BACKGROUND:Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptio...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-439

    authors: Chevenet F,Brun C,Bañuls AL,Jacq B,Christen R

    更新日期:2006-10-10 00:00:00

  • Projections for fast protein structure retrieval.

    abstract:BACKGROUND:In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniq...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-S5-S5

    authors: Bhattacharya S,Bhattacharyya C,Chandra NR

    更新日期:2006-12-18 00:00:00

  • PuFFIN--a parameter-free method to build nucleosome maps from paired-end reads.

    abstract:BACKGROUND:We introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing tools. In contrast to other approaches that require users to optimize several parameters according to t...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-15-S9-S11

    authors: Polishko A,Bunnik EM,Le Roch KG,Lonardi S

    更新日期:2014-01-01 00:00:00

  • ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.

    abstract:BACKGROUND:Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide "reverse engineering" of such networks have been successful only for lower eukaryotes with simple genomes. Here we present ARACNE, a n...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-S1-S7

    authors: Margolin AA,Nemenman I,Basso K,Wiggins C,Stolovitzky G,Dalla Favera R,Califano A

    更新日期:2006-03-20 00:00:00

  • SPIDer: Saccharomyces protein-protein interaction database.

    abstract:BACKGROUND:Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an important first step toward understanding cellular function and machinery of a proteome. Solely deri...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-S5-S16

    authors: Wu X,Zhu L,Guo J,Fu C,Zhou H,Dong D,Li Z,Zhang DY,Lin K

    更新日期:2006-12-18 00:00:00

  • Conceptual-level workflow modeling of scientific experiments using NMR as a case study.

    abstract:BACKGROUND:Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phase...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-31

    authors: Verdi KK,Ellis HJ,Gryk MR

    更新日期:2007-01-30 00:00:00

  • proTRAC--a software for probabilistic piRNA cluster detection, visualization and analysis.

    abstract:BACKGROUND:Throughout the metazoan lineage, typically gonadal expressed Piwi proteins and their guiding piRNAs (~26-32nt in length) form a protective mechanism of RNA interference directed against the propagation of transposable elements (TEs). Most piRNAs are generated from genomic piRNA clusters. Annotation of experi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-13-5

    authors: Rosenkranz D,Zischler H

    更新日期:2012-01-10 00:00:00

  • A genetic approach for building different alphabets for peptide and protein classification.

    abstract:BACKGROUND:In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm. The classification task is performed by a multi-classifier system where each classifier (Linear or Radial Basis function Support Vector Machines) is trained using feat...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-9-45

    authors: Nanni L,Lumini A

    更新日期:2008-01-24 00:00:00

  • GraphDNA: a Java program for graphical display of DNA composition analyses.

    abstract:BACKGROUND:Under conditions of no strand bias the number of Gs is equal to that of Cs for each DNA strand; similarly, the total number of Ts is equal to that of As. However, within each strand there are considerable local deviations from the A = T and G = C equality. These asymmetries in nucleotide composition have bee...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-21

    authors: Thomas JM,Horspool D,Brown G,Tcherepanov V,Upton C

    更新日期:2007-01-23 00:00:00

  • Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania.

    abstract:BACKGROUND:Leishmania and other members of the Trypanosomatidae family diverged early on in eukaryotic evolution and consequently display unique cellular properties. Their apparent lack of transcriptional regulation is compensated by complex post-transcriptional control mechanisms, including the processing of polycistr...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-9-158

    authors: Smith M,Blanchette M,Papadopoulou B

    更新日期:2008-03-20 00:00:00

  • CellSim: a novel software to calculate cell similarity and identify their co-regulation networks.

    abstract:BACKGROUND:Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regu...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-019-2699-3

    authors: Li L,Che D,Wang X,Zhang P,Rahman SU,Zhao J,Yu J,Tao S,Lu H,Liao M

    更新日期:2019-03-04 00:00:00

  • Quartet decomposition server: a platform for analyzing phylogenetic trees.

    abstract:BACKGROUND:The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-13-123

    authors: Mao F,Williams D,Zhaxybayeva O,Poptsova M,Lapierre P,Gogarten JP,Xu Y

    更新日期:2012-06-07 00:00:00

  • Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny.

    abstract:BACKGROUND:The rabbit is an important model organism used in a wide range of biomedical research. However, the rabbit genome is still sparsely annotated, thus prohibiting extensive functional analysis of gene sets derived from whole-genome experiments. We developed a web-based application that provides augmented annota...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-13-84

    authors: Craig DB,Kannan S,Dombkowski AA

    更新日期:2012-05-08 00:00:00

  • Improved functional prediction of proteins by learning kernel combinations in multilabel settings.

    abstract:BACKGROUND:We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of protein function. RESULTS:Explicit modeling of multilabels significantly improves the capability o...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-S2-S12

    authors: Roth V,Fischer B

    更新日期:2007-05-03 00:00:00

  • Bioinformatics approach to predict target genes for dysregulated microRNAs in hepatocellular carcinoma: study on a chemically-induced HCC mouse model.

    abstract:BACKGROUND:Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs that attract great attention because of their role in regulation of...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0836-1

    authors: Del Vecchio F,Gallo F,Di Marco A,Mastroiaco V,Caianiello P,Zazzeroni F,Alesse E,Tessitore A

    更新日期:2015-12-10 00:00:00

  • NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.

    abstract:BACKGROUND:Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes. However, deep coverage variations in short-read data sets and high sequencing error rates o...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-014-0357-3

    authors: McCorrison JM,Venepally P,Singh I,Fouts DE,Lasken RS,Methé BA

    更新日期:2014-11-19 00:00:00

  • GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.

    abstract:BACKGROUND:The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-016-1430-x

    authors: Tebel K,Boldt V,Steininger A,Port M,Ebert G,Ullmann R

    更新日期:2017-01-06 00:00:00

  • On reliable discovery of molecular signatures.

    abstract:BACKGROUND:Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods could yield valuable insight into cell biology and mechanisms of human disease. However, it is currently not clear how to control ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-38

    authors: Nilsson R,Björkegren J,Tegnér J

    更新日期:2009-01-29 00:00:00

  • Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data.

    abstract:BACKGROUND:This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulatio...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-13-310

    authors: Barros RC,Winck AT,Machado KS,Basgalupp MP,de Carvalho AC,Ruiz DD,de Souza ON

    更新日期:2012-11-21 00:00:00

  • Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking.

    abstract:BACKGROUND:The ability to detect nuclei in embryos is essential for studying the development of multicellular organisms. A system of automated nuclear detection has already been tested on a set of four-dimensional (4D) Nomarski differential interference contrast (DIC) microscope images of Caenorhabditis elegans embryos...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-6-125

    authors: Hamahashi S,Onami S,Kitano H

    更新日期:2005-05-24 00:00:00

  • ATMAD: robust image analysis for Automatic Tissue MicroArray De-arraying.

    abstract:BACKGROUND:Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembled onto a single support - ty...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-018-2111-8

    authors: Nguyen HN,Paveau V,Cauchois C,Kervrann C

    更新日期:2018-04-19 00:00:00