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 Bioinformaticsjournal_title
BMC bioinformaticsauthors
Clote P,Lou F,Lorenz WAdoi
10.1186/1471-2105-13-S5-S6subject
Has Abstractpub_date
2012-04-12 00:00:00pages
S6issn
1471-2105pii
1471-2105-13-S5-S6journal_volume
13 Suppl 5pub_type
杂志文章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
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更新日期:2006-06-02 00:00:00
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
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更新日期:2016-01-11 00:00:00
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...
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更新日期:2017-08-07 00:00:00
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journal_title:BMC bioinformatics
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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
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更新日期:2007-09-01 00:00:00
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
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更新日期:2010-06-15 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2015-05-28 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2006-10-10 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2006-12-18 00:00:00
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...
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pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-S1-S7
更新日期:2006-03-20 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-S5-S16
更新日期:2006-12-18 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-31
更新日期:2007-01-30 00:00:00
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
更新日期:2012-01-10 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2008-01-24 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2007-01-23 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-158
更新日期:2008-03-20 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2012-06-07 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2012-05-08 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2007-05-03 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2015-12-10 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2014-11-19 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2017-01-06 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2009-01-29 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2012-11-21 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2005-05-24 00:00:00
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更新日期:2018-04-19 00:00:00