Abstract：
:Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the lack of efficient and accurate experimental and computational methods for their characterization, which has largely hindered our understanding of many important biological processes. In this article, we describe a novel algorithm for genome-wide de novo prediction of CRBSs with high accuracy. We designed our algorithm to circumvent three identified difficulties for CRBS prediction using comparative genomics principles based on a new method for the selection of reference genomes, a new metric for measuring the similarity of CRBSs, and a new graph clustering procedure. When operon structures are correctly predicted, our algorithm can predict 81% of known individual binding sites belonging to 94% of known cis-regulatory motifs in the Escherichia coli K12 genome, while achieving high prediction specificity. Our algorithm has also achieved similar prediction accuracy in the Bacillus subtilis genome, suggesting that it is very robust, and thus can be applied to any other sequenced prokaryotic genome. When compared with the prior state-of-the-art algorithms, our algorithm outperforms them in both prediction sensitivity and specificity.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zhang S,Xu M,Li S,Su Zdoi
10.1093/nar/gkp248subject
Has Abstractpub_date
2009-06-01 00:00:00pages
e72issue
10eissn
0305-1048issn
1362-4962pii
gkp248journal_volume
37pub_type
杂志文章abstract：:Replacement of alpha-, beta- and gamma-phosphate groups in 2'-deoxynucleoside 5'-triphosphates (dNTP) with phosphonate groups yields a new set of dNTP mimics with potential biological and therapeutic applications. Here, we describe the synthesis of 15 new dNTPs modified at alpha-, beta- and gamma-phosphates containing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.3.778
更新日期：1998-02-01 00:00:00
abstract：:The two-step process of selection and counter-selection is a standard way to enable genetic modification and engineering of bacterial genomes using homologous recombination methods. The tetA and sacB genes are contained in a DNA cassette and confer a novel dual counter-selection system. Expression of tetA confers bact...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1075
更新日期：2013-12-01 00:00:00
abstract：:Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl255
更新日期：2006-07-01 00:00:00
abstract：:We present a simple and highly accurate computational method for operon prediction, based on intergenic distances and functional relationships between the protein products of contiguous genes, as defined by STRING database (Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq254
更新日期：2010-07-01 00:00:00
abstract：:A method to purify histone groups H2A+H2B and H3+H4 using dissociation with NaCl and hydroxylapatite chromatography is presented. The procedure is simple, involves mild solvents, and provides milligram quantities of histones of high purity. The histone pairs prepared by this method can regenerate chromatin-like charac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.2.689
更新日期：1979-02-01 00:00:00
abstract：:The ability to induce gene expression in a small molecule dependent manner has led to many applications in target discovery, functional elucidation and bio-production. To date these applications have relied on a limited set of protein-based control mechanisms operating at the level of transcription initiation. The dis...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv912
更新日期：2016-02-18 00:00:00
abstract：:Helicase-nuclease systems dedicated to DNA end resection in preparation for homologous recombination (HR) are present in all kingdoms of life. In thermophilic archaea, the HerA helicase and NurA nuclease cooperate with the highly conserved Mre11 and Rad50 proteins during HR-dependent DNA repair. Here we show that HerA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1157
更新日期：2012-04-01 00:00:00
abstract：:PIWI-interacting RNAs (piRNAs) comprise a class of small RNAs best known for suppressing transposable elements in germline tissues. The vector mosquito Aedes aegypti encodes seven PIWI genes, four of which are somatically expressed. This somatic piRNA pathway generates piRNAs from viral RNA during infection with cytop...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1266
更新日期：2019-03-18 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg392
更新日期：2003-06-01 00:00:00
abstract：:To examine the influence of thyrotropin (TSH) on the thyroglobulin (Tgb) mRNA content, the latter was evaluated in the cytoplasm of hog thyroid cells cultured in the absence (control cells) or presence of TSH. The Tgb mRNA levels were determined by, (i) kinetics of hybridization to sheep Tgb cDNA, (ii) capacity of cod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.10.3353
更新日期：1979-07-25 00:00:00
abstract：:The recognition of human tRNA(Leu) or tRNA(Ser) by cognate aminoacyl- tRNA synthetases has distinct requirements. Only one base change (A73-->G) in tRNA(Leu) is required to generate an efficient serine acceptor in vitro, whereas several changes in three structural domains (the acceptor stem, DHU loop and long extra ar...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.3.405
更新日期：1996-02-01 00:00:00
abstract：:HOX11 is a homeobox-containing oncogene of specific T-cell leukemias. We determined the DNA binding specificity of the Hox11 protein by using a novel technique of random oligonucleotide selection developed in this study. The optimal Hox11 binding sequence, GGCGGTAAGTGG, contained a core TAAGTG motif that is consistent...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.11.1928
更新日期：1995-06-11 00:00:00
abstract：:The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.23.7119
更新日期：1990-12-11 00:00:00
abstract：:Many small RNAs contribute essential activities to eukaryotic cells. In mammalian genomes dispersed repetitive sequences which exhibit homology to small RNAs often exist as pseudogenes which can complicate identification, localization, and analysis of the authentic gene. We mapped a productive human 7SK small nuclear ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.5.722
更新日期：1994-03-11 00:00:00
abstract：:Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky378
更新日期：2018-07-02 00:00:00
abstract：:The sequence of 110 nucleotides adjacent to the 3'-end of Neurospora crassa 25S-rRNA has been derived by chemical sequencing methods. Sequences present between 40 and 85 nucleotides of the 3'-end were found to complement sequences at the 3'- and 5'-ends of 5.8S-rRNA. Interaction was shown to occur between 5.8S-rRNA an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.5.1111
更新日期：1981-03-11 00:00:00
abstract：:The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa969
更新日期：2021-01-08 00:00:00
abstract：:Recently, a few Na+-specific RNA-cleaving DNAzymes were reported, where nucleobases are likely to play critical roles in catalysis. The NaA43 and NaH1 DNAzymes share the same 16-nt Na+-binding motif, but differ in one or two nucleotides in a small catalytic loop. Nevertheless, they display an opposite pH-dependency, i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz578
更新日期：2019-09-05 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw817
更新日期：2017-01-04 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.11.2223
更新日期：2001-06-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn524
更新日期：2008-10-01 00:00:00
abstract：:Homing endonucleases (HEs) cut long DNA target sites with high specificity to initiate and target the lateral transfer of mobile introns or inteins. This high site specificity of HEs makes them attractive reagents for gene targeting to promote DNA modification or repair. We have generated several hundred catalytically...
journal_title：Nucleic acids research
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doi：10.1093/nar/gkp004
更新日期：2009-04-01 00:00:00
abstract：:The integrases are a diverse family of tyrosine recombinases which rearrange DNA duplexes by means of conservative site-specific recombination reactions. Members of this family, of which the well-studied lambda Int protein is the prototype, were previously found to share four strongly conserved residues, including an ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.18.3605
更新日期：1997-09-15 00:00:00
abstract：:The high similarity of tunicates and vertebrates during their development coupled with the transparency of tunicate larvae, their well-studied cell lineages and the availability of simple and efficient transgenesis methods makes of this subphylum an ideal system for the investigation of vertebrate physiological and de...
journal_title：Nucleic acids research
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更新日期：2006-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.9.2313
更新日期：1992-05-11 00:00:00
abstract：:An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj515
更新日期：2006-03-17 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.17.3411
更新日期：1995-09-11 00:00:00
abstract：:Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-based multivariate statistical approach to the quantitative prediction of peptid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg510
更新日期：2003-07-01 00:00:00
abstract：:A simple method, primer specific and mispair extension analysis (PSMEA) with pfu DNA polymerase was developed for genotyping. PSMEA is based on the unique properties of 3'-->5' exonuclease proofreading activity. In the presence of an incomplete set of dNTPs, pfu was found to be extremely discriminative in nucleotide i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.21.5013
更新日期：1998-11-01 00:00:00
abstract：:The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli RR1 strain carrying the eco57IRM genes on a recombinant plasmid. The molecular weight of the denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with an apparent molecular weight of 104-1...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.22.6043
更新日期：1992-11-25 00:00:00
