BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.

abstract：:A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oli...

journal_title：Nucleic acids research

authors： Chartrand P,Harvey SC,Ferbeyre G,Usman N,Cedergren R

更新日期：1995-10-25 00:00:00

abstract：:The interpretation of data-driven experiments in genomics often involves a search for biological categories that are enriched for the responder genes identified by the experiments. However, knowledge bases such as the Gene Ontology (GO) contain hundreds or thousands of categories with very high overlap between categor...

journal_title：Nucleic acids research

authors： Bauer S,Gagneur J,Robinson PN

更新日期：2010-06-01 00:00:00

abstract：:The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis gr...

journal_title：Nucleic acids research

authors： Rose S,Auxilien S,Havelund JF,Kirpekar F,Huber H,Grosjean H,Douthwaite S

更新日期：2020-07-09 00:00:00

abstract：:This work describes the organization, at the nucleotide sequence level, of genes flanking the junctions of the large single copy regions and the inverted repeats of Spinacia oleracea (spinach) and Nicotiana debneyi chloroplast DNAs. In both genomes, trnH1, the gene for tRNA-His(GUG) is located at the extremity of the ...

journal_title：Nucleic acids research

authors： Zurawski G,Bottomley W,Whitfeld PR

更新日期：1984-08-24 00:00:00

abstract：:With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, we...

journal_title：Nucleic acids research

authors： Dilek A,Belviranli ME,Dogrusoz U

更新日期：2010-07-01 00:00:00

abstract：:The binary Cre-lox conditional knockout system requires an essential part of the target gene to be flanked by loxP sites, enabling excision in vivo upon Cre expression. LoxP sites are introduced by homologous recombination, together with a selectable marker. However, this marker can disturb gene expression and should ...

journal_title：Nucleic acids research

authors： Leneuve P,Colnot S,Hamard G,Francis F,Niwa-Kawakita M,Giovannini M,Holzenberger M

更新日期：2003-03-01 00:00:00

abstract：:In Xenopus oocytes, progesterone stimulates the cytoplasmic polyadenylation and resulting translational activation of c-mos mRNA, which is necessary for the induction of oocyte maturation. Although details of the biochemistry of polyadenylation are beginning to emerge, the mechanism by which 3' poly(A) addition stimul...

journal_title：Nucleic acids research

authors： Kuge H,Brownlee GG,Gershon PD,Richter JD

更新日期：1998-07-01 00:00:00

abstract：:Lambda-red system-based recombinogenic engineering is a powerful new method to engineer DNA without the need for restriction enzymes or ligases. Here, we report the use of a single selectable marker to enhance the usefulness of this approach. The strategy is to utilize the thymidylate synthase A (thyA) gene, which enc...

journal_title：Nucleic acids research

authors： Wong QN,Ng VC,Lin MC,Kung HF,Chan D,Huang JD

更新日期：2005-03-30 00:00:00

abstract：:We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. D...

journal_title：Nucleic acids research

authors： Zemla A

更新日期：2003-07-01 00:00:00

abstract：:Multiple sequence alignments play a central role in the annotation of novel genomes. Given the biological and computational complexity of this task, the automatic generation of high-quality alignments remains challenging. Since multiple alignments are usually employed at the very start of data analysis pipelines, it i...

journal_title：Nucleic acids research

authors： Lassmann T,Sonnhammer EL

更新日期：2005-12-16 00:00:00

abstract：:The hepatocyte nuclear factor (HNF)4alpha, a member of the nuclear receptor superfamily, regulates genes that play a critical role in embryogenesis and metabolism. Recent studies have shown that mutations in the human HNF4alpha gene cause a rare form of type 2 diabetes, maturity onset diabetes of the young (MODY1). To...

journal_title：Nucleic acids research

authors： Lausen J,Thomas H,Lemm I,Bulman M,Borgschulze M,Lingott A,Hattersley AT,Ryffel GU

更新日期：2000-01-15 00:00:00

abstract：:Proteins that catalyse homologous recombination have been identified in all living organisms and are essential for the repair of damaged DNA as well as for the generation of genetic diversity. In bacteria homologous recombination is performed by the RecA protein, whereas in the eukarya a related protein called Rad51 i...

journal_title：Nucleic acids research

authors： McIlwraith MJ,Hall DR,Stasiak AZ,Stasiak A,Wigley DB,West SC

更新日期：2001-11-15 00:00:00

abstract：:Non-protein-coding RNAs (ncRNAs) fulfill a wide range of cellular functions from protein synthesis to regulation of gene expression. Identification of novel regulatory ncRNAs by experimental approaches commonly includes the generation of specialized cDNA libraries encoding small ncRNA species. However, such identifica...

journal_title：Nucleic acids research

authors： Mrázek J,Kreutmayer SB,Grässer FA,Polacek N,Hüttenhofer A

更新日期：2007-01-01 00:00:00

abstract：:We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction o...

journal_title：Nucleic acids research

authors： Guye P,Li Y,Wroblewska L,Duportet X,Weiss R

更新日期：2013-09-01 00:00:00

abstract：:To screen multiple loci in small purified samples of diploid and aneuploid cells a PCR-based technique of whole genome amplification was adapted to the study of somatic lesions. DNA samples from different numbers of flow-sorted diploid and aneuploid cells from biopsies were amplified with a degenerate 15mer primer. Al...

journal_title：Nucleic acids research

authors： Barrett MT,Reid BJ,Joslyn G

更新日期：1995-09-11 00:00:00

abstract：:A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not ...

journal_title：Nucleic acids research

authors： Wu J,Anczuków O,Krainer AR,Zhang MQ,Zhang C

更新日期：2013-05-01 00:00:00

abstract：:A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' U...

journal_title：Nucleic acids research

authors： Halperin Y,Linhart C,Ulitsky I,Shamir R

更新日期：2009-04-01 00:00:00

abstract：:Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. These enzymes have been shown to control several biological functions in the bacterial cells. In recent years biochemical studies, sequence analyses and structure reso...

journal_title：Nucleic acids research

authors： Jadeau F,Grangeasse C,Shi L,Mijakovic I,Deléage G,Combet C

更新日期：2012-01-01 00:00:00

abstract：:The Saccharomyces cerevisiae viruses are non-infectious double-stranded (ds) RNA viruses present in most laboratory strains of yeast. Their genome consists of one or more dsRNAs separately encapsidated in particles composed mainly of one polypeptide, which has a Mr of 88 kdaltons in the best-studied viral subtype. A l...

journal_title：Nucleic acids research

authors： Bruenn J,Madura K,Siegel A,Miner Z,Lee M

更新日期：1985-03-11 00:00:00

abstract：:Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...

journal_title：Nucleic acids research

authors： Howes G,O'Connor M,Chia W

更新日期：1988-04-11 00:00:00

abstract：:The wobble uridine of certain bacterial and mitochondrial tRNAs is modified, at position 5, through an unknown reaction pathway that utilizes the evolutionarily conserved MnmE and GidA proteins. The resulting modification (a methyluridine derivative) plays a critical role in decoding NNG/A codons and reading frame mai...

journal_title：Nucleic acids research

authors： Moukadiri I,Prado S,Piera J,Velázquez-Campoy A,Björk GR,Armengod ME

更新日期：2009-11-01 00:00:00

abstract：:Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast...

journal_title：Nucleic acids research

authors： Ståhlberg A,Krzyzanowski PM,Jackson JB,Egyud M,Stein L,Godfrey TE

更新日期：2016-06-20 00:00:00

abstract：:The crystal structure is reported of a complex between an ethyl derivative of the minor-groove drug furamidine and the dodecanucleotide duplex d(CGCGAATTCGCG)2, which has been refined to 1.85 A resolution and an R factor of 16.6% for data collected at -173 degreesC. An exceptionally large number (220) of water molecul...

journal_title：Nucleic acids research

authors： Guerri A,Simpson IJ,Neidle S

更新日期：1998-06-15 00:00:00

abstract：:Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library prepa...

journal_title：Nucleic acids research

authors： Harkins KM,Schaefer NK,Troll CJ,Rao V,Kapp J,Naughton C,Shapiro B,Green RE

更新日期：2020-05-07 00:00:00

abstract：:The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of no...

journal_title：Nucleic acids research

authors： Grosjean H,Westhof E

更新日期：2016-09-30 00:00:00

abstract：:Human foamy or spuma virus (HFV) codes for a distinct set of pol gen products. To determine the minimal requirements for the HFV enzymatic activities, defined residues of the reverse transcriptase (RT) and ribo-nuclease H (RNase H) domain of the HFV pol gene were mutated by site-specific PCR mutagenesis. The mutant ge...

journal_title：Nucleic acids research

authors： Kögel D,Aboud M,Flügel RM

更新日期：1995-07-25 00:00:00

abstract：:Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, her...

journal_title：Nucleic acids research

authors： Yan Y,Zhang D,Zhou P,Li B,Huang SY

更新日期：2017-07-03 00:00:00

abstract：:Recently, a family of transcription factors structurally related to Sp1 has been described; thus, more than one activator may bind to the GC boxes present in a number of viral and cellular promoters. We have compared the transactivation potentials of Sp1, Sp3 and Sp4 proteins on the human immunodeficiency virus type 1...

journal_title：Nucleic acids research

authors： Majello B,De Luca P,Hagen G,Suske G,Lania L

更新日期：1994-11-25 00:00:00

abstract：:We have developed efficient methods for creating artificial transposons and inserting these transposons into plasmid targets in vitro, primarily for the purpose of DNA mapping and sequencing. A novel plasmid has been engineered to convert virtually any DNA sequence, or combination of sequences, into an artificial tran...

journal_title：Nucleic acids research

authors： Devine SE,Boeke JD

更新日期：1994-09-11 00:00:00

abstract：:Short repetitive DNA sequences are believed to be one of the primordial genetic elements that served as a source of complex large DNA found in the genome of modern organisms. However, the mechanism of its expansion (increase in repeat number) during the course of evolution is unclear. We demonstrate that the DNA polym...

journal_title：Nucleic acids research

authors： Ogata N,Morino H

更新日期：2000-10-15 00:00:00