Abstract:
:Transcription is the first step in gene expression, and it is the step at which most of the regulation of expression occurs. Although sequenced prokaryotic genomes provide a wealth of information, transcriptional regulatory networks are still poorly understood using the available genomic information, largely because accurate prediction of promoters is difficult. To improve promoter recognition performance, a novel variable-window Z-curve method is developed to extract general features of prokaryotic promoters. The features are used for further classification by the partial least squares technique. To verify the prediction performance, the proposed method is applied to predict promoter fragments of two representative prokaryotic model organisms (Escherichia coli and Bacillus subtilis). Depending on the feature extraction and selection power of the proposed method, the promoter prediction accuracies are improved markedly over most existing approaches: for E. coli, the accuracies are 96.05% (σ(70) promoters, coding negative samples), 90.44% (σ(70) promoters, non-coding negative samples), 92.13% (known sigma-factor promoters, coding negative samples), 92.50% (known sigma-factor promoters, non-coding negative samples), respectively; for B. subtilis, the accuracies are 95.83% (known sigma-factor promoters, coding negative samples) and 99.09% (known sigma-factor promoters, non-coding negative samples). Additionally, being a linear technique, the computational simplicity of the proposed method makes it easy to run in a matter of minutes on ordinary personal computers or even laptops. More importantly, there is no need to optimize parameters, so it is very practical for predicting other species promoters without any prior knowledge or prior information of the statistical properties of the samples.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Song Kdoi
10.1093/nar/gkr795subject
Has Abstractpub_date
2012-02-01 00:00:00pages
963-71issue
3eissn
0305-1048issn
1362-4962pii
gkr795journal_volume
40pub_type
杂志文章abstract::Plants have large diverse families of small secreted proteins (SSPs) that play critical roles in the processes of development, differentiation, defense, flowering, stress response, symbiosis, etc. Oryza sativa is one of the major crops worldwide and an excellent model for monocotyledonous plants. However, there had no...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1090
更新日期:2013-01-01 00:00:00
abstract::Polyadenylation is a co-transcriptional process that modifies mRNA 3'-ends in eukaryotes. In yeast, CF IA and CPF constitute the core 3'-end maturation complex. CF IA comprises Rna14p, Rna15p, Pcf11p and Clp1p. CF IA interacts with the C-terminal domain of RNA Pol II largest subunit via Pcf11p which links pre-mRNA 3'-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr800
更新日期:2012-02-01 00:00:00
abstract::Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh736
更新日期:2004-08-03 00:00:00
abstract::Plasmids containing a dihydrofolate reductase (DHFR) expression unit were transfected into DHFR-deficient Chinese hamster ovary (CHO) cells. Methotrexate exposure was used to select cells with amplified DHFR sequences. Three cell lines were isolated containing amplified copies of transfected DNA that had integrated in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.4.1697
更新日期:1989-02-25 00:00:00
abstract::The centromere complex is a multicomponent structure essential for faithful chromosome transmission. Here we show that the S. cerevisiae centromere protein Cpf1 bends centromere DNA element I (CDEI) with the bend angle ranging from 66 degrees to 71 degrees. CDEI DNA sequences that carry point mutations which lead to r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.20.4726
更新日期:1993-10-11 00:00:00
abstract::An enzyme capable of liberating functional tRNA(Lys) from Escherichia coli diacetyl-lysyl-tRNA(Lys) was purified from the archae Sulfolobus solfataricus. Contrasting with the specificity of peptidyl- tRNA hydrolase (PTH) from E.coli, the S.solfataricus enzyme readily accepts E.coli formyl-methionyl-tRNA(fMet) as a sub...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg428
更新日期:2003-06-15 00:00:00
abstract::The RNA of a deleted strain (lacking Src gene) of an avian sarcoma virus (ASV) was examined by a newly developed immunoelectron microscopic procedure which uses anti-nucleotide antibodies as probes. After denaturation of the RNA and reaction with a high affinity, highly specific anti-7-methylguanosine-5'-phosphate (an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.19.4485
更新日期:1980-10-10 00:00:00
abstract::Xenbase (www.xenbase.org), the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is the principal centralized resource of genomic, development data and community information for Xenopus research. Recent improvements include the addition of the literature and interaction tabs to gene catalog page...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp953
更新日期:2010-01-01 00:00:00
abstract::M13 RF IV DNA may be prepared in vitro to contain phosphorothioate-modified internucleotidic linkages in the (-)strand only. Certain restriction enzymes react with this modified DNA to hydrolyze the (+)strand exclusively when a phosphorothioate linkage occurs at the normal cleavage point in the (-)strand. The reaction...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.24.8765
更新日期:1985-12-20 00:00:00
abstract::We describe a cell-free chromatin assembly system derived from the yeast Saccharomyces cerevisiae, which efficiently packages DNA into minichromosomes in a reaction dependent on exogenous core histones and an ATP-regenerating system. Both supercoiled and relaxed plasmid DNA serve as templates for nucleosomal loading i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh107
更新日期:2004-07-28 00:00:00
abstract::Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes witho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx572
更新日期:2017-08-21 00:00:00
abstract::Immunoglobulin (Ig) diversification by somatic hypermutation in germinal center B cells is instrumental for maturation of the humoral immune response, but also bears the risk of excessive or aberrant genetic changes. Thus, introduction of DNA damage by activation-induced cytidine deaminase as well as DNA repair by mul...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1378
更新日期:2014-04-01 00:00:00
abstract::Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs ensure both accurate RNA recognition and the efficient catalysis of aminoacylation. The effects of tRNA(Trp)variants on the aminoacylation reaction catalyzed by wild-type Escherichia coli tryptophanyl-tRNA synthe-tase (TrpRS) hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.18.3631
更新日期:1999-09-15 00:00:00
abstract::Two hexamer DNA fragments containing a carcinogenic modified base, O6-methyl guanine, have been synthesized by a solid-phase phosphotriester method, in which the unmodified guanine residues present were O6 protected with the 4-nitrophenylethyl group. These two alkylated oligonucleotides were found to have similar Tm's...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.10.3393
更新日期:1983-05-25 00:00:00
abstract::The rat beta-casein gene is a member of a small gene family, encoding the principal milk proteins. In order to understand the mechanisms by which its stage- and tissue-specific expression are regulated, initially, a 14 kb genomic clone containing the entire 7.5 kb rat beta-casein gene with 3.5 kb of 5' and 3.0 kb of 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.3.1027
更新日期:1988-02-11 00:00:00
abstract::A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkz124
更新日期:2019-04-23 00:00:00
abstract::The unknown modified nucleotide G*, isolated from both Schizosaccharomyces pombe and Torulopsis utilis initiator tRNAs(Met), has been identified as an O-ribosyl-(1"----2')-guanosine-5"-phosphate, called Gr(p), by means of HPLC, UV-absorption, mass spectrometry and periodate oxidation procedures. By comparison with the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5199
更新日期:1991-10-11 00:00:00
abstract::The restriction endonuclease (R.BsuFI) of Bacillus subtilis recognizes the target DNA sequence 5' CCGG. The R.BsuFI gene was found in close proximity to the cognate M.BsuFI gene, which had previously been characterized (1). Cloning of the R.BsuFI gene in E.coli was only possible with the M.BsuFI Mtase gene present on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.23.6457
更新日期:1991-12-11 00:00:00
abstract::Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2723
更新日期:1998-06-01 00:00:00
abstract::The dhp1+ gene of Schizosaccharomyces pombe is a homolog of Saccharomyces cerevisiae HKE1/RAT1/TAP1 gene that is involved in RNA metabolism such as RNA trafficking and RNA synthesis. dhp1+ is also related to S. cerevisiae DST2 (SEP1) that encodes a DNA strand exchange protein required for sporulation and homologous re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.357
更新日期:1995-02-11 00:00:00
abstract::The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). The number of families has grown substantially to a total of 17,929 in release 32.0. New additions have been coupled with efforts to improve existing families, including refinement of domain boundaries, their classification into Pfa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky995
更新日期:2019-01-08 00:00:00
abstract::The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.1.22
更新日期:2001-01-01 00:00:00
abstract::We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh363
更新日期:2004-07-01 00:00:00
abstract::RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward understanding the basic mechanisms of the post-transcriptional gene regulation. Though numerous computational methods have been dev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1025
更新日期:2016-02-29 00:00:00
abstract::The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification ex...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki073
更新日期:2005-01-01 00:00:00
abstract::The DNA damage checkpoint halts cell cycle progression in G2 in response to genotoxic insults. Central to the execution of cell cycle arrest is the checkpoint-induced stabilization of securin-separase complex (yeast Pds1-Esp1). The checkpoint kinases Chk1 and Chk2 (yeast Chk1 and Rad53) are thought to critically contr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa355
更新日期:2020-06-19 00:00:00
abstract::The glycoprotein C (gC) gene of herpes simplex virus type 1 is a true late gene, in that its expression occurs late in infection with a strict requirement for viral DNA replication. Recently, we reported on gC expression during infection with mutant viruses carrying deletions in the gC gene promoter. Analysis of RNA e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.7.3097
更新日期:1987-04-10 00:00:00
abstract::The Escherichia coli AlkB protein catalyzes the direct reversal of alkylation damage to DNA; primarily 1-methyladenine (1mA) and 3-methylcytosine (3mC) lesions created by endogenous or environmental alkylating agents. AlkB is a member of the non-heme iron (II) alpha-ketoglutarate-dependent dioxygenase superfamily, whi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1031
更新日期:2007-01-01 00:00:00
abstract::Phage display technology involves the display of proteins or peptides, as coat protein fusions, on the surface of a phage or phagemid particles. Using standard technology, helper phage are essential for the replication and assembly of phagemid particles, during library production and biopanning. We have eliminated the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl772
更新日期:2006-01-01 00:00:00
abstract::The active form of Escherichia coli DNA polymerase V responsible for damage-induced mutagenesis is a multiprotein complex (UmuD'(2)C-RecA-ATP), called pol V Mut. Optimal activity of pol V Mut in vitro is observed on an SSB-coated single-stranded circular DNA template in the presence of the β/γ complex and a transactiv...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks233
更新日期:2012-07-01 00:00:00