Abstract：
:RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accuracy for longer sequences. A heuristic approach is to search for promising pseudoknot candidates in a sequence and verify those. Afterwards, the detected pseudoknots can be further analysed using bioinformatics or laboratory techniques. We present a novel pseudoknot detection method called DotKnot that extracts stem regions from the secondary structure probability dot plot and assembles pseudoknot candidates in a constructive fashion. We evaluate pseudoknot free energies using novel parameters, which have recently become available. We show that the conventional probability dot plot makes a wide class of pseudoknots including those with bulged stems manageable in an explicit fashion. The energy parameters now become the limiting factor in pseudoknot prediction. DotKnot is an efficient method for long sequences, which finds pseudoknots with higher accuracy compared to other known prediction algorithms. DotKnot is accessible as a web server at http://dotknot.csse.uwa.edu.au.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sperschneider J,Datta Adoi
10.1093/nar/gkq021subject
Has Abstractpub_date
2010-04-01 00:00:00pages
e103issue
7eissn
0305-1048issn
1362-4962pii
gkq021journal_volume
38pub_type
杂志文章abstract：:Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1245
更新日期：2019-02-20 00:00:00
abstract：:We present NetCore, a novel network propagation approach based on node coreness, for phenotype-genotype associations and module identification. NetCore addresses the node degree bias in PPI networks by using node coreness in the random walk with restart procedure, and achieves improved re-ranking of genes after propag...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa639
更新日期：2020-09-25 00:00:00
abstract：:A UCSD Pascal program was developed which can analyze nucleic acid dot matrices of up to 9500 X 9500 in size on the Apple II computer. Although matrices of such size consume large amounts of computer memory, this program minimizes these problems by analyzing only small strips of the matrix at a time, and then transfer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.767
更新日期：1984-01-11 00:00:00
abstract：:The archaeal exosome is a phosphorolytic 3'-5' exoribonuclease complex. In a reverse reaction it synthesizes A-rich RNA tails. Its RNA-binding cap comprises the eukaryotic orthologs Rrp4 and Csl4, and an archaea-specific subunit annotated as DnaG. In Sulfolobus solfataricus DnaG and Rrp4 but not Csl4 show preference f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku969
更新日期：2014-11-10 00:00:00
abstract：:The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). Access to promoter sequences is provided by pointers to positions in the corresponding genomes. Promoter evidence comes from conventional TSS mappi...
journal_title：Nucleic acids research
pub_type： 历史文章,杂志文章
doi：10.1093/nar/gkj146
更新日期：2006-01-01 00:00:00
abstract：:Activation of the transcription factor NF-kappaB is critical for the tumor necrosis factor-alpha (TNF-alpha)-induced inflammatory response. Here we report the complete gene expression profile from activated microvascular endothelial cells emphasizing the direct contribution of the NF-kappaB pathway. Human microvascula...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki836
更新日期：2005-09-21 00:00:00
abstract：:We studied in vivo transcription and gene expression directed by a series of synthetic sequences, bearing the consensus hexamer (CH) pair of E.coli promoters in various contexts. The results demonstrate that, for the contexts tested, the CH pair supports transcription activity and gene expression, whether the spacer l...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.5.1137
更新日期：1990-03-11 00:00:00
abstract：:Partial acid cleavage, comparative HPLC tryptic peptide mapping and amino acid sequencing of the C1 and C2 proteins of HeLa heterogeneous nuclear ribonucleoprotein (hnRNP) particles demonstrate that proteins C1 and C2 differ in primary structure by the presence of a 13 amino acid insert sequence in C2. This C2 insert ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.21.8441
更新日期：1989-11-11 00:00:00
abstract：:Circular DNA aptamers are powerful candidates for therapeutic applications given their dramatically enhanced biostability. Herein we report the first effort to evolve circular DNA aptamers that bind a human protein directly in serum, a complex biofluid. Targeting human thrombin, this strategy has led to the discovery ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa800
更新日期：2020-11-04 00:00:00
abstract：:DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 880 115 entries or 1 134 086 245 bases in the period from July 2006 to June 2007. The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others. Our computer system has been upgraded since March 2007. Anoth...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm889
更新日期：2008-01-01 00:00:00
abstract：:Aberration within the p53 tumor suppressor gene is the most frequently identified genetic damage in human cancer. Regulatory functions proposed for the p53 protein include modulation of the cell cycle, cellular differentiation, signal transduction, and gene expression. Additionally, the p53 gene product may guard the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.3.713
更新日期：1993-02-11 00:00:00
abstract：:A downstream G-rich sequence (GRS), GGGGGAGGUGUGGG, has been previously shown to influence the efficiency of 3' end processing of the SV40 late polyadenylation signal. We have now defined several important parameters for GRS-mediated polyadenylation. The ability of the GRS to influence 3' end processing efficiency was...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.9.1625
更新日期：1995-05-11 00:00:00
abstract：:To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw782
更新日期：2016-12-15 00:00:00
abstract：:We have constructed deletion mutants of simian virus 40 (SV40) lacking the two tandemly repeated copies or all three copies of the 21-bp repeated sequence located in the origin region. The mutants were viable, but had lower infectivities compared to the wild type. The mutant lacking two copies of the 21-bp repeat grew...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.5.1601
更新日期：1983-03-11 00:00:00
abstract：:Approximately half of all human transcripts contain at least one upstream translational initiation site that precedes the main coding sequence (CDS) and gives rise to an upstream open reading frame (uORF). We generated uORFdb, publicly available at http://cbdm.mdc-berlin.de/tools/uorfdb, to serve as a comprehensive li...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt952
更新日期：2014-01-01 00:00:00
abstract：:Methods for increasing the transient level of expression of transfected DNA in cultured Drosophila cells have been examined. Here we show that cells exposed to the steroid hormone 20-hydroxyecdysone for 48h prior to transfection show an 4 to 5 fold increase in the levels of expression of transfected DNA. By analysis, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.22.9255
更新日期：1987-11-25 00:00:00
abstract：:Characterization of the ability of human interferons (IFNs) to rapidly induce genes led to the identification of the first two members of the STAT (signal transducers and activators of transcription) family, Stat1 and Stat2. To study the unique role of this transcription factor in IFN signaling under more physiologica...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.21.4191
更新日期：1999-11-01 00:00:00
abstract：:G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that R...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa442
更新日期：2020-07-09 00:00:00
abstract：:Loading of the replicative ring helicase onto the origin of replication (oriC) is the final outcome of a well coordinated series of events that collectively constitute a primosomal cascade. Once the ring helicase is loaded, it recruits the primase and signals the switch to the polymerization mode. The transient nature...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh628
更新日期：2004-06-01 00:00:00
abstract：:It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological part...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv464
更新日期：2015-07-27 00:00:00
abstract：:Ribosome biogenesis is a key process for maintaining protein synthetic capacity in dividing or growing cells, and requires coordinated production of ribosomal proteins and ribosomal RNA (rRNA), including the processing of the latter. Signalling through mammalian target of rapamycin complex 1 (mTORC1) activates all the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku130
更新日期：2014-04-01 00:00:00
abstract：:The rapidly growing amount of genomic sequence data being generated and made publicly available necessitate the development of new data storage and archiving methods. The vast amount of data being shared and manipulated also create new challenges for network resources. Thus, developing advanced data compression techni...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks709
更新日期：2012-11-01 00:00:00
abstract：:ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy datab...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1108
更新日期：2018-01-04 00:00:00
abstract：:Myotonic dystrophy type 1 (DM1) is caused by the expansion of a (CTG).(CAG) repeat in the DMPK gene on chromosome 19q13.3. At least 17 neurological diseases have similar genetic mutations, the expansion of DNA repeats. In most of these disorders, the disease severity is related to the length of the repeat expansion, a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh976
更新日期：2004-12-01 00:00:00
abstract：:In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-β-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 Å and 2.80 Å reso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv732
更新日期：2015-09-18 00:00:00
abstract：:The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz898
更新日期：2020-01-08 00:00:00
abstract：:DNase I and MPE.Fe (II) footprinting both employ partial cleavage of ligand-protected DNA restriction fragments and Maxam-Gilbert sequencing gel methods of analysis. One method utilizes the enzyme, DNase I, as the DNA cleaving agent while the other employs the synthetic molecule, methidium-propyl-EDTA (MPE). For actin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.16.5555
更新日期：1983-08-25 00:00:00
abstract：:Allostery is comprehensively studied for natural macromolecules, such as proteins and nucleic acids. Here, we present controllable allostery of synthetic DNA nanostructure-enzyme systems. Rational designs of the synthetic allosteric systems are based on an in-depth understanding of allosteric sites with several types ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa488
更新日期：2020-07-27 00:00:00
abstract：:RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks289
更新日期：2012-08-01 00:00:00
abstract：:Escherichia coli leucyl-tRNA synthetase (LeuRS) aminoacylates up to six different class II tRNA(leu) molecules. Each has a distinct anticodon and varied nucleotides in other regions of the tRNA. Attempts to construct a minihelix RNA that can be aminoacylated with leucine have been unsuccessful. Herein, we describe the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.10.2103
更新日期：2002-05-15 00:00:00
