Abstract:
:The 'regions' method for multisequence alignment used in the previously reported program MALIGN has been generalized to include recursive refinement so that unaligned portions between two regions at the current level of resolution can be handled with increased resolution. Additionally, there is incorporated a limiting of the number of regions to be used at any level of resolution from which to abstract an alignment. This provides a significant increase in speed over the unlimited version. The program GENALIGN uses this improved regions method to execute fast pairwise alignments in the framework of Taylor's multisequence alignment procedure using clustered pairwise alignments. Pairwise alignments by dynamic programming are also provided in the program.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Martinez HMdoi
10.1093/nar/16.5.1683subject
Has Abstractpub_date
1988-03-11 00:00:00pages
1683-91issue
5eissn
0305-1048issn
1362-4962journal_volume
16pub_type
杂志文章abstract::Anti-microRNA (miRNA) oligonucleotides (AMOs) with 2'-O-Methyl (2'OMe) residues are commonly used to study miRNA function and can achieve high potency, with low cytotoxicity. Not withstanding this, we demonstrate the sequence-dependent capacity of 2'OMe AMOs to inhibit Toll-like receptor (TLR) 7 and 8 sensing of immun...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1343
更新日期:2015-01-01 00:00:00
abstract::The diverse localization of transcripts in cells suggests that there are many specific RNA-protein interactions that have yet to be identified. Progress has been limited, however, by the lack of a robust method to detect and isolate the RNA-binding proteins. Here we describe the use of an RNA aptamer, scaffolded to a ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1316
更新日期:2011-04-01 00:00:00
abstract::Several different computational problems have been solved using DNA as a medium. However, the DNA computations that have so far been carried out have examined a relatively small number of possible sequence solutions in order to find correct sequence solutions. We have encoded a search algorithm in DNA that required th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.22.5203
更新日期:1998-11-15 00:00:00
abstract::Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv311
更新日期:2015-05-19 00:00:00
abstract::Expression of the rpoBC genes encoding the beta and beta' RNA polymerase subunits of Escherichia coli is autogenously regulated. Although previous studies have demonstrated a post-transcriptional feedback mechanism, complex transcriptional controls of rpoBC expression may also contribute. We show that an attenuator (r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.18.4773
更新日期:1992-09-25 00:00:00
abstract::Applications of conditional gene expression, whether for therapeutic or basic research purposes, are increasingly requiring mammalian gene control systems that exhibit far tighter control properties. While numerous approaches have been used to improve the widely used Tet-regulatory system, many applications, particula...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn443
更新日期:2008-09-01 00:00:00
abstract::Augmented biological activity in vitro has been demonstrated in oligonucleotides (oligos) modified to provide nuclease resistance, to enhance cellular uptake or to increase target affinity. How chemical modification affects the duration of effect of an oligo with potent activity has not been investigated directly. We ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.6.977
更新日期:1994-03-25 00:00:00
abstract::H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address thes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks773
更新日期:2012-10-01 00:00:00
abstract::The nucleotide sequence of a T4 tRNA with an anticodon for glycine has been determined using (32)P-labeled material from T4-infected cultures of Escherichiacoli. The sequence is: pGCGGAUAUCGUAUAAUGmGDAUUACCUCAGACUUCCAApsiCUGAUGAUGUGAGTpsiCGAUUCUCAUUAUCCGCUCCA-OH. The 74 nucleotide sequence can be arranged in the class...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.10.1287
更新日期:1974-10-01 00:00:00
abstract::We have examined the behaviour of the beta-interferon promoter in mouse F9 embryonal carcinoma cells. In undifferentiated cells, the beta-interferon promoter is not responsive to dsRNA or to Sendai virus. In cells stimulated to differentiate into parietal endoderm by treatment with retinoic acid, the beta-interferon p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.21.4489
更新日期:1994-10-25 00:00:00
abstract::A number of cysteine-rich proteins have recently been isolated by homology screening, differential library screens, and association with other proteins. In this report, we describe the isolation of the rat cysteine-rich protein from a rat brain library during a search for clones with homology to the delta-opioid recep...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.24.5477
更新日期:1994-12-11 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::Exon arrays are regularly used to analyze differential splicing events. GeneChip Gene 1.0 ST Arrays (gene arrays) manufactured by Affymetrix, Inc. are primarily used to determine expression levels of transcripts, although their basic design is rather similar to GeneChip Exon 1.0 ST Arrays (exon arrays). Here, we show ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1110
更新日期:2012-03-01 00:00:00
abstract::A somatic cell hybrid line containing only human chromosome 21 on a mouse background has been used as the source of DNA for construction of a recombinant phage library. Individual phages containing human inserts have been identified. Repeat-free human DNA subclones have been prepared and used to screen for restriction...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.17.6075
更新日期:1985-09-11 00:00:00
abstract::Pathbase is a database that stores images of the abnormal histology associated with spontaneous and induced mutations of both embryonic and adult mice including those produced by transgenesis, targeted mutagenesis and chemical mutagenesis. Images of normal mouse histology and strain-dependent background lesions are al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh124
更新日期:2004-01-01 00:00:00
abstract::Contrary to the expectation, the Merrifield polystyrene resin, 2% cross-linked by divinylbenzene, is as efficient as the polyacrylmorpholide resin for the synthesis of polydeoxyribonucleotides using a phosphotriester method. On the Merrifield resin, the tetradecamer, dTpCpGpTpCpApApCpTpGpGpCpTpT, and the hexadecamer, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.22.5507
更新日期:1980-11-25 00:00:00
abstract::The mRNAs for different variant surface antigens of Trypanosoma brucei start with the same 35 nucleotides. This sequence is encoded by a separate mini-exon, located in a 1.35-kb repetitive element. We have reported that trypanosomes contain many transcripts that hybridize to mini-exon probes, even if they do not make ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.3777
更新日期:1984-05-11 00:00:00
abstract::RNA synthesis and DNA replication cease after DNA damage. We studied RNA synthesis using an in situ run-on assay and found ribosomal RNA (rRNA) synthesis was inhibited 24 h after UV light, gamma radiation or DNA cross-linking by cisplatin in human cells. Cisplatin led to accumulation of cells in S phase. Inhibition of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt502
更新日期:2013-08-01 00:00:00
abstract::We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa015
更新日期:2020-03-18 00:00:00
abstract::Apurinic/apyrimidinic endonuclease 1 (APE1), an essential protein in mammals, is involved in base excision DNA repair (BER) and in regulation of gene expression, acting as a redox co-activator of several transcription factors. Recent findings highlight a novel role for APE1 in RNA metabolism, which is modulated by nuc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq691
更新日期:2010-12-01 00:00:00
abstract::The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.292
更新日期:2000-01-01 00:00:00
abstract::Spliceosomes are assembled in stages. The first stage forms complex E, which is characterized by the presence of U1 snRNPs base-paired to the 5' splice site, components recognizing the 3' splice site and proteins thought to connect them. The splice sites are held in close proximity and the pre-mRNA is committed to spl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks322
更新日期:2012-08-01 00:00:00
abstract::The high mobility group protein (HMG)-box is a DNA-binding domain found in many proteins that bind preferentially to DNA of irregular structures in a sequence-independent manner and can bend the DNA. We show here that GST-fusion proteins of HMG domains from HMG1 and HMG2 promote a triple-stranded complex formation bet...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.23.4733
更新日期:1996-12-01 00:00:00
abstract::Human transcription factor IIIC contains a 55 kDa polypeptide which specifically interacts with the Adenovirus 2 VAI gene promoter and which mimics most of the DNA binding properties of the entire factor. The specificity and affinity of this protein:DNA interaction was demonstrated by: (i) Separation of purified fract...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.16.4743
更新日期:1990-08-25 00:00:00
abstract::Calf thymus DNA polymerase alpha (pol alpha) and bacteriophage T4 DNA polymerase (pol T4) were exploited as model enzymes to investigate the molecular mechanism of inhibitory action of N2-(p-n-butylphenyl)dGTP (BuPdGTP) and 2-(p-n-butyl-anilino)dATP (BuAdATP) on the BuPdNTP-susceptible alpha polymerase family. Kinetic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.7.1627
更新日期:1991-04-11 00:00:00
abstract::The catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) is a member of a sub-family of phosphatidylinositol (PI) 3-kinases termed PIK-related kinases. A distinguishing feature of this sub-family is the presence of a conserved C-terminal region downstream of a PI 3-kinase domain. Mutants defective in DNA-P...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.8.1965
更新日期:1998-04-15 00:00:00
abstract::Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular assemblies. It is a modular protein, rich in large potentially unfolded ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1166
更新日期:2012-04-01 00:00:00
abstract::Aryldiazonium salts are shown to be useful as phototriggered structural probes for RNA mapping as well as for footprinting of RNA/protein interaction. In particular the yeast tRNA(Asp)/aspartyl-tRNA synthetase complex is shown to involve the variable loop face and the concave side of the L-shaped nucleic acid bound to...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.1.89
更新日期:1990-01-11 00:00:00
abstract::Ornithine decarboxylase (ODC) expression is important for proliferation and is elevated in many tumor cells. We previously showed that Sp1 is a major positive regulator of ODC transcription. In this paper we have investigated transcriptional regulation of rat ODC by the closely related factor Sp3. While over-expressio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.10.2012
更新日期:1997-05-15 00:00:00
abstract::The replication origin (oriC) of the Escherichia coli chromosome has been cloned and the region essential for chromosomal replication has been delimited to 245 base pairs. In previous studies the ability of recombinants between oriC and ColE1-type vectors, to transform E. coli polA- strains was used to determine which...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.22.8007
更新日期:1983-11-25 00:00:00