当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > DDBJ new system and service refactoring.

DDBJ new system and service refactoring.

Abstract：

:The DNA data bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) maintains a primary nucleotide sequence database and provides analytical resources for biological information to researchers. This database content is exchanged with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Resources provided by the DDBJ include traditional nucleotide sequence data released in the form of 27 316 452 entries or 16 876 791 557 base pairs (as of June 2012), and raw reads of new generation sequencers in the sequence read archive (SRA). A Japanese researcher published his own genome sequence via DDBJ-SRA on 31 July 2012. To cope with the ongoing genomic data deluge, in March 2012, our computer previous system was totally replaced by a commodity cluster-based system that boasts 122.5 TFlops of CPU capacity and 5 PB of storage space. During this upgrade, it was considered crucial to replace and refactor substantial portions of the DDBJ software systems as well. As a result of the replacement process, which took more than 2 years to perform, we have achieved significant improvements in system performance.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Ogasawara O,Mashima J,Kodama Y,Kaminuma E,Nakamura Y,Okubo K,Takagi T

doi

10.1093/nar/gks1152

subject

Has Abstract

pub_date

2013-01-01 00:00:00

pages

D25-9

issue

Database issue

eissn

0305-1048

issn

1362-4962

pii

gks1152

journal_volume

41

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Identification of essential domains for Escherichia coli tRNA(leu) aminoacylation and amino acid editing using minimalist RNA molecules.

    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

    authors： Larkin DC,Williams AM,Martinis SA,Fox GE

    更新日期：2002-05-15 00:00:00

  • Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

    abstract：:The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa;...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx932

    authors： Lefkowitz EJ,Dempsey DM,Hendrickson RC,Orton RJ,Siddell SG,Smith DB

    更新日期：2018-01-04 00:00:00

  • Enhancing identification of cancer types via lowly-expressed microRNAs.

    abstract：:The primary function of microRNAs (miRNAs) is to maintain cell homeostasis. In cancerous tissues miRNAs' expression undergo drastic alterations. In this study, we use miRNA expression profiles from The Cancer Genome Atlas of 24 cancer types and 3 healthy tissues, collected from >8500 samples. We seek to classify the c...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx210

    authors： Rasnic R,Linial N,Linial M

    更新日期：2017-05-19 00:00:00

  • Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology.

    abstract：:Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; howev...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz1173

    authors： Zhou W,Emery SB,Flasch DA,Wang Y,Kwan KY,Kidd JM,Moran JV,Mills RE

    更新日期：2020-02-20 00:00:00

  • Organization of the 3'-boundary of the chicken alpha globin gene domain and characterization of a CR 1-specific protein binding site.

    abstract：:The sequence of a DNA fragment about 1 Kbp long located at the 3' boundary of the chicken alpha globin gene domain, including the 3'-side matrix attachment point and the site of transcription termination, was determined. It contains a repetitive DNA element and the AT-rich (easily denaturable) DNA segment conserved at...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/18.3.401

    authors： Farache G,Razin SV,Targa FR,Scherrer K

    更新日期：1990-02-11 00:00:00

  • MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features.

    abstract：:A fundamental problem with applying Consensus, Weight-Matrix or hidden Markov models as search tools for biosequences is that there is no way to know, from the model, if the modeled sequences display any dependencies between positional identities. In some instances, these dependencies are crucial in correctly acceptin...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gki374

    authors： Ray WC

    更新日期：2005-07-01 00:00:00

  • The PARP promoter of Trypanosoma brucei is developmentally regulated in a chromosomal context.

    abstract：:African trypanosomes are extracellular protozoan parasites that are transmitted from one mammalian host to the next by tsetse flies. Bloodstream forms express variant surface glycoprotein (VSG); the tsetse fly (procyclic) forms express instead the procyclic acidic repetitive protein (PARP). PARP mRNA is abundant in pr...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/24.7.1202

    authors： Biebinger S,Rettenmaier S,Flaspohler J,Hartmann C,Peña-Diaz J,Wirtz LE,Hotz HR,Barry JD,Clayton C

    更新日期：1996-04-01 00:00:00

  • Role of PCNA-dependent stimulation of 3'-phosphodiesterase and 3'-5' exonuclease activities of human Ape2 in repair of oxidative DNA damage.

    abstract：:Human Ape2 protein has 3' phosphodiesterase activity for processing 3'-damaged DNA termini, 3'-5' exonuclease activity that supports removal of mismatched nucleotides from the 3'-end of DNA, and a somewhat weak AP-endonuclease activity. However, very little is known about the role of Ape2 in DNA repair processes. Here...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp357

    authors： Burkovics P,Hajdú I,Szukacsov V,Unk I,Haracska L

    更新日期：2009-07-01 00:00:00

  • An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain.

    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

    pub_type： 杂志文章

    doi：10.1093/nar/23.20.4092

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

    更新日期：1995-10-25 00:00:00

  • An open reading frame upstream from the nifH gene of Klebsiella pneumoniae.

    abstract：:An open reading frame upstream from nifHDK operon of Klebsiella pneumoniae had been described. The orientation of this open reading frame is opposite to that of nifHDK and sequence homology was found between the open reading frame promoter and the promoter of nifHDK operon. A recombinant plasmid carrying the promoter ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/11.12.4241

    authors： Shen SC,Xue ZT,Kong QI,Wu QL

    更新日期：1983-06-25 00:00:00

  • Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana.

    abstract：:We present MultiGO, a web-enabled tool for the identification of biologically relevant gene sets from hierarchically clustered gene expression trees (http://ekhidna.biocenter.helsinki.fi/poxo/multigo). High-throughput gene expression measuring techniques, such as microarrays, are nowadays often used to monitor the exp...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl694

    authors： Kankainen M,Brader G,Törönen P,Palva ET,Holm L

    更新日期：2006-01-01 00:00:00

  • SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.

    abstract：:SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv351

    authors： Dereeper A,Homa F,Andres G,Sempere G,Sarah G,Hueber Y,Dufayard JF,Ruiz M

    更新日期：2015-07-01 00:00:00

  • Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog.

    abstract：:A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many ca...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw736

    authors： Spring-Connell AM,Evich MG,Debelak H,Seela F,Germann MW

    更新日期：2016-10-14 00:00:00

  • A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation.

    abstract：:RNA polymerase (RNAP) is a major target of gene regulation. Thermus thermophilus bacteriophage P23-45 encodes two RNAP binding proteins, gp39 and gp76, which shut off host gene transcription while allowing orderly transcription of phage genes. We previously reported the structure of the T. thermophilus RNAP•σA holoenz...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx1162

    authors： Ooi WY,Murayama Y,Mekler V,Minakhin L,Severinov K,Yokoyama S,Sekine SI

    更新日期：2018-01-09 00:00:00

  • Interaction of human telomeric DNA with N-methyl mesoporphyrin IX.

    abstract：:The remarkable selectivity of N-methyl mesoporphyrin IX (NMM) for G-quadruplexes (GQs) is long known, however its ability to stabilize and bind GQs has not been investigated in detail. Through the use of circular dichroism, UV-visible spectroscopy and fluorescence resonance energy transfer (FRET) melting assay we have...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks152

    authors： Nicoludis JM,Barrett SP,Mergny JL,Yatsunyk LA

    更新日期：2012-07-01 00:00:00

  • Reorganizing the protein space at the Universal Protein Resource (UniProt).

    abstract：:The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr981

    authors： UniProt Consortium.

    更新日期：2012-01-01 00:00:00

  • Complete nucleotide sequence of the fumarase gene (citG) of Bacillus subtilis 168.

    abstract：:The nucleotide sequence of a 2.14 kb fragment of Bacillus subtilis DNA containing the citG gene encoding fumarase was determined using the dideoxy chain termination method. The citG coding region of 1392 base pairs (464 codons) was identified, and the deduced Mr (50425) is in good agreement with that of the protein id...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/13.1.131

    authors： Miles JS,Guest JR

    更新日期：1985-01-11 00:00:00

  • Antisense-induced ribosomal frameshifting.

    abstract：:Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1-ORF2...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl531

    authors： Henderson CM,Anderson CB,Howard MT

    更新日期：2006-01-01 00:00:00

  • Organization, structure and expression of murine interferon alpha genes.

    abstract：:Using a human interferon-alpha probe we have isolated recombinant phages containing murine interferon-alpha (Mu IFN-alpha) genes from a genomic library. One of these phages contained two complete Mu IFN-alpha genes and part of a third gene. The insert of a second phage held two IFN genes. This indicates that the Mu IF...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/13.3.791

    authors： Zwarthoff EC,Mooren AT,Trapman J

    更新日期：1985-02-11 00:00:00

  • A computer program to enter DNA gel reading data into a computer.

    abstract：:This paper describes a simple program that uses a digitizing device to enter DNA sequences directly from autoradiographs into a computer. ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/12.1part2.499

    authors： Staden R

    更新日期：1984-01-11 00:00:00

  • Elongation of repetitive DNA by DNA polymerase from a hyperthermophilic bacterium Thermus thermophilus.

    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

    pub_type： 杂志文章

    doi：10.1093/nar/28.20.3999

    authors： Ogata N,Morino H

    更新日期：2000-10-15 00:00:00

  • Overexpression of the base excision repair NTHL1 glycosylase causes genomic instability and early cellular hallmarks of cancer.

    abstract：:Base excision repair (BER), which is initiated by DNA N-glycosylase proteins, is the frontline for repairing potentially mutagenic DNA base damage. The NTHL1 glycosylase, which excises DNA base damage caused by reactive oxygen species, is thought to be a tumor suppressor. However, in addition to NTHL1 loss-of-function...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky162

    authors： Limpose KL,Trego KS,Li Z,Leung SW,Sarker AH,Shah JA,Ramalingam SS,Werner EM,Dynan WS,Cooper PK,Corbett AH,Doetsch PW

    更新日期：2018-05-18 00:00:00

  • Primer specific and mispair extension analysis (PSMEA) as a simple approach to fast genotyping.

    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

    authors： Hu YW,Balaskas E,Kessler G,Issid C,Scully LJ,Murphy DG,Rinfret A,Giulivi A,Scalia V,Gill P

    更新日期：1998-11-01 00:00:00

  • Regulation of the small regulatory RNA MicA by ribonuclease III: a target-dependent pathway.

    abstract：:MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1239

    authors： Viegas SC,Silva IJ,Saramago M,Domingues S,Arraiano CM

    更新日期：2011-04-01 00:00:00

  • Cell type-specific genomics of Drosophila neurons.

    abstract：:Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks671

    authors： Henry GL,Davis FP,Picard S,Eddy SR

    更新日期：2012-10-01 00:00:00

  • DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.

    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 accura...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq021

    authors： Sperschneider J,Datta A

    更新日期：2010-04-01 00:00:00

  • In situ hybridization with fluoresceinated DNA.

    abstract：:We have used fluorescein-11-dUTP in a nick-translation format to produce fluoresceinated human nucleic acid probes. After in situ hybridization of fluoresceinated DNAs to human metaphase chromosomes, the detection sensitivity was found to be 50-100 kb. The feasibility and the increase in detection sensitivity of micro...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.12.3237

    authors： Wiegant J,Ried T,Nederlof PM,van der Ploeg M,Tanke HJ,Raap AK

    更新日期：1991-06-25 00:00:00

  • MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data.

    abstract：:MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-seq results with the goal of providing an integrated resource for mammalian transcriptional regulation and epigenetics. We analyzed 507 million uniquely aligned RNAP-II ChIP-seq reads from 26 differ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1171

    authors： Gupta R,Bhattacharyya A,Agosto-Perez FJ,Wickramasinghe P,Davuluri RV

    更新日期：2011-01-01 00:00:00

  • Cloning of human satellite III DNA: different components are on different chromosomes.

    abstract：:Two fragments cloned from purified human satellite III DNA do not cross-react with each other. One fragment, for which a partial sequence is reported, hybridises to satellite II as well as III and is shown to originate on chromosome 1. The other cloned fragment originates from the Y chromosome. This fragment has under...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/6.10.3177

    authors： Cooke HJ,Hindley J

    更新日期：1979-07-25 00:00:00

  • Structural determinants of an internal ribosome entry site that direct translational reading frame selection.

    abstract：:The dicistrovirus intergenic internal ribosome entry site (IGR IRES) directly recruits the ribosome and initiates translation using a non-AUG codon. A subset of IGR IRESs initiates translation in either of two overlapping open reading frames (ORFs), resulting in expression of the 0 frame viral structural polyprotein a...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku622

    authors： Ren Q,Au HH,Wang QS,Lee S,Jan E

    更新日期：2014-08-01 00:00:00