Abstract:
:The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kitts PA,Church DM,Thibaud-Nissen F,Choi J,Hem V,Sapojnikov V,Smith RG,Tatusova T,Xiang C,Zherikov A,DiCuccio M,Murphy TD,Pruitt KD,Kimchi Adoi
10.1093/nar/gkv1226subject
Has Abstractpub_date
2016-01-04 00:00:00pages
D73-80issue
D1eissn
0305-1048issn
1362-4962pii
gkv1226journal_volume
44pub_type
杂志文章abstract::We recently compared the efficiency of six picornaviral internal ribosome entry segments (IRESes) and the hepatitis C virus (HCV) IRES for their ability to drive internal initiation of translationin vitro. Here we present the results of a similar comparison performed in six different cultured cell lines infected with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.5.925
更新日期:1997-03-01 00:00:00
abstract::In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Ut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1172
更新日期:2011-01-01 00:00:00
abstract::No analogous nucleoside triphosphate was found which acts as well as ATP in binding to and supporting catalysis of leucyl-tRNA synthetase from Escherichia coli MRE 600. However, there are numerous nucleotides which are able to replace ATP, but with lower efficiency. The 6-amino group of the adenine ring and the 2'-hyd...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.8.2067
更新日期:1976-08-01 00:00:00
abstract::The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing infor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl793
更新日期:2007-01-01 00:00:00
abstract::Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku923
更新日期:2014-11-10 00:00:00
abstract::Nucleosomes, a basic structural unit of eukaryotic chromatin, play a significant role in regulating gene expression. We have developed a web tool based on DNA sequences known from empirical and theoretical studies to influence DNA bending and flexibility, and to exclude nucleosomes. NXSensor (available at http://www.s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl158
更新日期:2006-07-01 00:00:00
abstract::Although the promoters of both the Bax and p21 genes are activated by p53, they differ in the effect on this activation of the POU family transcription factor Brn-3a. Thus, Brn-3a inhibits activation of the Bax promoter by p53 but enhances the ability of p53 to activate the p21 promoter. We demonstrate that repression...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf610
更新日期:2002-11-15 00:00:00
abstract::Despite much information as to the structure and function of the general transcription factors, little is known about the regulation of their expression. Transcription of the Saccharomyces cerevisiae SUA7 (TFIIB) gene results in the formation of two discrete transcripts. It was originally reported that the two transcr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.22.4435
更新日期:2000-11-15 00:00:00
abstract::Elucidating the dynamic organization of nuclear RNA foci is important for understanding and manipulating these functional sites of gene expression in both physiological and pathological states. However, such studies have been difficult to establish in vivo as a result of the absence of suitable RNA imaging methods. He...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv614
更新日期:2015-10-30 00:00:00
abstract::A new class of synthetic DNA duplexes containing repeating oligonucleotide sequences, double-helical concatemers, is characterized. The UV-absorption and circular dichroism of a concatemer formed in self-association of d(T-G-C-A-C-A-T-G) have been studied. The thermodynamical parameters of complex formation are the fo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.11.2413
更新日期:1980-06-11 00:00:00
abstract::Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.3.695
更新日期:2000-02-01 00:00:00
abstract::The presence of the C.C mispair in a defined duplex oligodeoxynucleotide enhanced its capacity to serve as a substrate for highly purified human DNA methyltransferase. Analysis of tritiated reaction products showed that the C.C mispair acted as a "methylation acceptor" in that it was itself rapidly methylated. The m5C...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.17.6899
更新日期:1987-09-11 00:00:00
abstract::Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across tax...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1060
更新日期:2018-01-04 00:00:00
abstract::The complete mitochondrial (mt) genome of Crossostoma lacustre, a freshwater loach from mountain stream of Taiwan, has been cloned and sequenced. This fish mt genome, consisting of 16558 base-pairs, encodes genes for 13 proteins, two rRNAs, and 22 tRNAs, in addition to a regulatory sequence for replication and transcr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.18.4853
更新日期:1992-09-25 00:00:00
abstract::The highly charged DNA chain may be either in an extended conformation, the coil, or condensed into a highly dense and ordered structure, the toroid. The transition, also called collapse of the chain, can be triggered in different ways, for example by changing the ionic conditions of the solution. We observe individua...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1494
更新日期:2016-02-18 00:00:00
abstract::We previously showed that histone H4 serine-1 phosphorylation (H4S1ph) is evolutionarily conserved during gametogenesis, and contributes to post-meiotic nuclear compaction and to full completion of sporulation in the yeast Saccharomyces cerevisiae. Previous studies showed that H4S1ph and another modification of the sa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq218
更新日期:2010-08-01 00:00:00
abstract::This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw256
更新日期:2016-07-08 00:00:00
abstract::A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem-loop II. In a previous study we demonstrated that a minizyme with high activity forms a dimeric structure with a common stem II. Because of their dimeric structure, minizymes are potentially capable of cleaving a substrate at two di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.12.2302
更新日期:1996-06-15 00:00:00
abstract::Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz181
更新日期:2019-05-21 00:00:00
abstract::In the poly(A)+RNA isolated from the ciliate Paramecium primaurelia is found a discrete and abundant mRNA species of high molecular weight (corresponding to about 9,000 nucleotides). This mRNA species has size and abundance characteristics that identify it tentatively as the message coding for the variant cell-surface...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.21.7375
更新日期:1983-11-11 00:00:00
abstract::DNA swivel (nicking-rejoining) enzyme activity has been studied in various cell fractions of a human lymphoid cell line. Swivel activity is found only in chromatin and in a nuclear membrane fraction containing DNA and possessing endogenous DNA synthesizing activity. Twenty percent of the total swivel activity and less...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.1.223
更新日期:1977-01-01 00:00:00
abstract::A recently reported cDNA clone coding for human promyelocytic L apoferritin, shows some differences with a liver L apoferritin cDNA. We have investigated if these differences are due to the expression of different genes or to an alternative transcription of an unique gene. In this paper we report data suggesting that ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.7.2863
更新日期:1986-04-11 00:00:00
abstract::Helicase loading at a DNA replication origin often requires the dynamic interactions between the DNA helicase and an accessory protein. In E. coli, the DNA helicase is DnaB and DnaC is its loading partner. We used the method of hydrogen/deuterium exchange mass spectrometry to address the importance of DnaB-DnaC comple...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv961
更新日期:2016-01-08 00:00:00
abstract::We have investigated the mechanism of the electrophoresis-driven chromatin aggregation which had been described by Weintraub (1984, Cell 38, 17-27) as a putative mean for propagation of genetic repression in eukaryotes. We show that the oligonucleosome aggregates are assembled de novo at the starting zone of DNP elect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.24.7397
更新日期:1990-12-25 00:00:00
abstract::We have previously investigated the role of the N-terminal region of ribosomal protein S4 to participate in 30S ribosome assembly and function (1-3). In this report we extend these studies to the two fragments produced by the chemical cleavage of protein S4 at the tryptophan residue 167. We find that the carboxyl term...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.17.6343
更新日期:1985-09-11 00:00:00
abstract::Foldback DNA, prepared from mouse and Scilla sibirica main band DNA, and from rye (Secale cereale) total DNA, was characterised by denaturation, renaturation, and electron microscopy. 3H-cRNA of this DNA was hybridised in situ to nuclei and chromosomes of the respective species. There is no universal labelling pattern...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.10.3589
更新日期:1978-10-01 00:00:00
abstract::We have characterized triple-helix-mediated inhibition of an artificial bacteriophage promoter with respect to relief of inhibition by incoming RNA polymerases that initiate upstream or downstream from the operator sequence. Whereas oligonucleotide-directed triple-helix formation inhibits the test promoter, promoter a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.17.4055
更新日期:1993-08-25 00:00:00
abstract::A new integrated image analysis package with quantitative quality control schemes is described for cDNA microarray technology. The package employs an iterative algorithm that utilizes both intensity characteristics and spatial information of the spots on a microarray image for signal-background segmentation and define...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.15.e75
更新日期:2001-08-01 00:00:00
abstract::A prototype of a novel class of DNA alkylating agents, which combines the DNA crosslinking moiety chlorambucil (Chl) with a sequence-selective hairpin pyrrole-imidazole polyamide ImPy-beta-ImPy-gamma-ImPy-beta-Dp (polyamide 1), was evaluated for its ability to damage DNA and induce biological responses. Polyamide 1-Ch...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg215
更新日期:2003-02-15 00:00:00
abstract::Activating sequence factor 1 (ASF-1) is a nuclear DNA-binding activity that is found in monocots and dicots. It interacts with several TGACG-containing elements that have been characterized from viral and T-DNA genes, the prototypes of which are the as-1 element of the CaMV 35S promoter and the ocs element from the oc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.18.3778
更新日期:1995-09-25 00:00:00