Abstract：
:With discovery of diverse roles for RNA, its centrality in cellular functions has become increasingly apparent. A number of algorithms have been developed to predict RNA secondary structure. Their performance has been benchmarked by comparing structure predictions to reference secondary structures. Generally, algorithms are compared against each other and one is selected as best without statistical testing to determine whether the improvement is significant. In this work, it is demonstrated that the prediction accuracies of methods correlate with each other over sets of sequences. One possible reason for this correlation is that many algorithms use the same underlying principles. A set of benchmarks published previously for programs that predict a structure common to three or more sequences is statistically analyzed as an example to show that it can be rigorously evaluated using paired two-sample t-tests. Finally, a pipeline of statistical analyses is proposed to guide the choice of data set size and performance assessment for benchmarks of structure prediction. The pipeline is applied using 5S rRNA sequences as an example.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Xu Z,Almudevar A,Mathews DHdoi
10.1093/nar/gkr1081subject
Has Abstractpub_date
2012-02-01 00:00:00pages
e26issue
4eissn
0305-1048issn
1362-4962pii
gkr1081journal_volume
40pub_type
杂志文章abstract：:Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx376
更新日期：2017-07-03 00:00:00
abstract：:DNA polymerase lambda (pol lambda) is a member of the X family DNA polymerases and is endowed with multiple enzymatic activities. In this work we investigated the in vitro miscoding properties of full-length, human pol lambda either in the absence or in the presence of the human auxiliary proteins proliferating cell n...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl032
更新日期：2006-03-06 00:00:00
abstract：:Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until ...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkj469
更新日期：2006-01-25 00:00:00
abstract：:Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essentia...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1165
更新日期：2017-01-25 00:00:00
abstract：:Use of the polymerase chain reaction (PCR) to amplify variable numbers of tandem repeat (VNTR) loci has become widely used in genetic typing. Unfortunately, preferential amplification of small allelic products relative to large allelic products may result in incorrect or ambiguous typing in a heterozygous sample. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.15.3050
更新日期：1995-08-11 00:00:00
abstract：:An improved contact hybridization technique for the analysis of labelled RNA species is presented. The method combines high sensitivity of detection with the high resolution of polyacrylamide gel electrophoresis and should be especially useful for the characterization of transient RNA precursor molecules. Its applicat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.9.2963
更新日期：1979-07-11 00:00:00
abstract：:A multipurpose plasmid, pUR 250, has been constructed. It contains seven unique cloning sites (Hind III, Xba I, Sal I, Acc I, Hinc II, BamH I and EcoR I) in a small region of its lac Z gene part. Insertion of foreign DNA into the plasmid can be easily detected. Plasmid DNA isolated from a clone by a rapid method can b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.19.5765
更新日期：1982-10-11 00:00:00
abstract：:A very mild and efficient procedure has been developed for the preparation of C-5 substituted deoxyuridines. The substituent carries a masked primary aliphatic amino group. These compounds are readily converted into their phosphoramidites and can be used to prepare oligonucleotides carrying one or more aliphatic amino...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.12.4857
更新日期：1987-06-25 00:00:00
abstract：:The genome of the cell is often exposed to DNA damaging agents and therefore requires an intricate well-regulated DNA damage response (DDR) to overcome its deleterious effects. The DDR needs proper regulation for its timely activation, repression, as well as appropriate choice of repair pathway. Studies in Saccharomyc...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkw1369
更新日期：2017-03-17 00:00:00
abstract：UNLABELLED:The PubMed® database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have im...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku432
更新日期：2014-07-01 00:00:00
abstract：:The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences are both eukaryotic and archaeal in origin. Several new histone fold-containing proteins have been identified, includin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.320
更新日期：2000-01-01 00:00:00
abstract：:The promoter region of the mouse CCAAT-Enhancer Binding Protein (C/EBP alpha) gene is capable of directing high levels of expression of reporter constructs in various cell lines, albeit even in cells that do not express their endogenous C/EBP alpha gene. To understand the molecular mechanisms underlying this ubiquitou...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.8.1735
更新日期：1993-04-25 00:00:00
abstract：:The deoxyribose hexanucleoside pentaphosphate (m5dC-dG)3 has been studied by 500 MHz 1H NMR in D2O (0.1 M NaCl) and in D2O/deuterated methanol mixtures. Two conformations, in slow equilibrium on the NMR time scale, were detected in methanolic solution. Two-dimensional nuclear Overhauser effect (NOE) experiments were u...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.2.1243
更新日期：1984-01-25 00:00:00
abstract：:Previous studies have implicated the DE-1 (-111/-106) and alpha A-CRYBP1 (-66/-57) sites for activity of the mouse alpha A-crystallin promoter in transiently transfected lens cells. Here we have used the bacterial chloramphenicol acetyltransferase (CAT) reporter gene to test the functional importance of the putative D...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.11.2633
更新日期：1993-06-11 00:00:00
abstract：:Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a large number of economically-significant crops. Traditional 'dot-blot hybridization' or PCR-based assays for identifyin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.7.e23
更新日期：2000-04-01 00:00:00
abstract：:Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt165
更新日期：2013-05-01 00:00:00
abstract：:Saccharomyces cerevisiae Pif1 (ScPif1) is known as an ATP-dependent DNA helicase that plays critical roles in a number of important biological processes such as DNA replication, telomere maintenance and genome stability maintenance. Besides its DNA helicase activity, ScPif1 is also known as a single-stranded DNA (ssDN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz541
更新日期：2019-08-22 00:00:00
abstract：:We have developed a web-based resource (available at www.ciliate.org) for researchers studying the model ciliate organism Tetrahymena thermophila. Employing the underlying database structure and programming of the Saccharomyces Genome Database, the Tetrahymena Genome Database (TGD) integrates the wealth of knowledge g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj054
更新日期：2006-01-01 00:00:00
abstract：:Synthesis of a small amount of 42S RNA in addition to the VSV specific mRNA species was observed in a coupled transcription-translation system containing ribonucleoprotein particles from L cell infected with vesicular stomatitis virus and nuclease-treated ribosomal extract obtained from uninfected HeLa cells. Analysis...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.20.6341
更新日期：1982-10-25 00:00:00
abstract：:DNA synthesized by in vitro transcription on rat interferon (IFN) mRNA has been cloned and amplified as recombinant DNA. The nucleotide sequence of these rat IFN cDNA clones revealed i. the partial presence of the coding region of the gene and ii all cDNA clones were derived from the same subtype of rat IFN-alpha mRNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.2.1227
更新日期：1984-01-25 00:00:00
abstract：:The interaction of RNase T1 with calf thymus DNA was studied using uv difference spectroscopy and the effect of the enzyme on DNA melting. There was no indication of RNase T1 binding with native DNA. A prominent difference spectrum for RNase T1 binding with denatured DNA (d-DNA) was observed at pH 5, 25 degrees and lo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.1.11
更新日期：1975-01-01 00:00:00
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pub_type： 杂志文章
doi：10.1093/nar/gkl958
更新日期：2007-01-01 00:00:00
abstract：:Chromatin fragments released from intact Friend erythroleukemia cell nuclei during limited incubation with micrococcal nuclease, DNase II or DNase I were analyzed to determine the distribution of DNA methyltransferase in chromatin. The enzyme was released in a free form when internucleosomal DNA was digested with micr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.20.5359
更新日期：1981-10-24 00:00:00
abstract：:Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt636
更新日期：2013-10-01 00:00:00
abstract：:Understanding the cellular uptake and intracellular trafficking of dendrimer-DNA complexes is an important prerequisite for improving the transfection efficiency of non-viral vector-mediated gene delivery. Dendrimers are synthetic polymers used for gene transfer. Although these cationic molecules show promise as versa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh595
更新日期：2004-05-17 00:00:00
abstract：:A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emissi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx942
更新日期：2017-12-01 00:00:00
abstract：:TcruziDB (http://TcruziDB.org) is an integrated genome database for the parasitic organism Trypanosoma cruzi, the causative agent of Chagas' disease. The database currently incorporates all available sequence data (Genomic, BAC, EST) in a single user-friendly location. The database contains a variety of tools specific...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh049
更新日期：2004-01-01 00:00:00
abstract：:Stability of aromatic phosphoramidates was studied using 2',3'-O-dibenzoyluridine 5'-phosphoramidates and N,2',3'-O-tribenzoylcytidine 5'-phosphate. The effect of dicyclohexylcarbodiimide in this mixture was investigated. Decomposition of the anilidate was slower in the presence of DCC. Substituted anilidates of uridi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.2.223
更新日期：1974-02-01 00:00:00
abstract：:Equilibrium and kinetics of thermal melting of yeast 5S ribosomal RNA in aqueous NaCl with or without Mg2+ were investigated by differential thermal melting and temperature jump methods. Two peaks (1 and 2) and a shoulder were observed in each of melting curves at ionic strength I=0.002-0.5 and linearity between each ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.10.3363
更新日期：1983-05-25 00:00:00
abstract：:The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. orde...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm800
更新日期：2008-01-01 00:00:00
