Abstract:
:We have previously described programs for a variety of types of sequence analysis (1-4). These programs have now been integrated into a single package. They are written in the standard C programming language and run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running under the MS/DOS and UNIX operating systems. The programs are widely distributed and may be obtained from the authors as described below.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Mount DW,Conrad Bdoi
10.1093/nar/14.1.443subject
Has Abstractpub_date
1986-01-10 00:00:00pages
443-54issue
1eissn
0305-1048issn
1362-4962journal_volume
14pub_type
杂志文章abstract::Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky510
更新日期:2018-07-02 00:00:00
abstract::The structures of the termini and their flanking regions of two human KpnI family members were investigated. The two differed in length, but the starting sequence at one terminal (defined as the 5' terminal) was found to be common to both members. The Alu family sequence was found in the 5' flanking regions. The KpnI ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.19.6837
更新日期:1983-10-11 00:00:00
abstract::The paper presents measurements of the difference in the melting temperature of a colE1 DNA region when it is located inside the DNA helix and at its end. A direct comparison of calculations based on the rigorous theory of helix-coil transition with experimental data for .2 M Na+ (the conditions for fully reversible m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.20.5469
更新日期:1981-10-24 00:00:00
abstract::Secondary structure-sensitive chemical and enzymatic probes have been used to produce a model for the folding of the last 68 residues of the 3'-non-coding region of beet necrotic yellow vein benevirus RNA 3. The structure consists of two stem-loops separated by a single-stranded region. RNA 3-derived transcripts were ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.23.4723
更新日期:1997-12-01 00:00:00
abstract::The 4.5S rRNA was isolated from the chloroplast ribosomes from Dryopteris acuminata. The complete nucleotide sequence was determined to be: OHUAAGGUCACGGCAAGACGAGCCGUUUAUCACCACGAUAGGUGCUAAGUGGAGGUGCAGUAAUGUAUGCAGCUGAGGC AUCCUAAUAGACCGAGAGGUUUGAACOH. The 4.5S rRNA is composed of 103 nucleotides and shows strong homolog...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.7.2257
更新日期:1982-04-10 00:00:00
abstract::Eukaryotic cells possess several distinct mismatch repair pathways. A mismatch can be introduced in retroviral double-stranded DNA by a pre-existing mutation within the primer binding site (PBS) of the viral RNA genome. In order to evaluate mismatch repair of retroviral double-stranded DNA, Moloney leukemia virus (MLV...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.12.2302
更新日期:2000-06-15 00:00:00
abstract::A dinucleoside monophosphate, 6,2'-anhydro-6-oxy-1-beta-D-arabinofuranosyluracil-phosphoryl- (3'-5')-6,2'-anhydro-6-oxy-1-beta-D-arabinofuranosyluracil (I) was synthesized by the condensation reaction using DCC from 5'-monomethoxytrityl derivative(VII) and 3'-acetyl-5'-phosphate(X) of the monomer units. Yield was ca. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.3.479
更新日期:1974-03-01 00:00:00
abstract::Traditional chromatin analysis methods only test one locus at the time or use different templates for each locus, making a standardized analysis of large genomic regions or many co-regulated genes at different loci a difficult task. On the other hand, genome-wide high-resolution mapping of chromatin accessibility empl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp037
更新日期:2009-04-01 00:00:00
abstract::Members of the basic helix-loop-helix (bHLH) family of transcription factors regulate a wide array of developmental processes in many cell types, including cell fate specification, differentiation and morphogenesis. Our studies describe the cloning of a gene from the nematode Caenorhabditis elegans that is closely rel...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.21.4423
更新日期:2001-11-01 00:00:00
abstract::The kinetics of PaeR7 endonuclease-catalysed cleavage reactions of fluorophor-labeled oligonucleotide substrates have been examined using fluorescence resonance energy transfer (FRET). A series of duplex substrates were synthesized with an internal CTCGAG PaeR7 recognition site and donor (fluorescein) and acceptor (rh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.3155
更新日期:1994-08-11 00:00:00
abstract::Oligoribonucleotides containing a 5'-phosphorothiolate linkage have provided effective tools to study the mechanisms of RNA catalysis, allowing resolution of kinetic ambiguity associated with mechanistic dissection and providing a strategy to establish linkage between catalysis and specific functional groups. However,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1265
更新日期:2011-03-01 00:00:00
abstract::Inducible promoters are a central regulatory component in synthetic biology, metabolic engineering, and protein production for laboratory and commercial uses. Many of these applications utilize two or more exogenous promoters, imposing a currently unquantifiable metabolic burden on the living system. Here, we engineer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa734
更新日期:2020-09-25 00:00:00
abstract::Optimization of primer sequences for polymerase chain reaction (PCR) and quantitative PCR (qPCR) and reaction conditions remains an experimental challenge. We have developed a resource, PrimerBank, which contains primers that can be used for PCR and qPCR under stringent and allele-invariant amplification conditions. A...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1013
更新日期:2012-01-01 00:00:00
abstract::VapD-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3D structure of these proteins. Recently, a relationship between the Cas2 family of ribonucleases associated with the CRISPR system of microbial immunity and VapD was suggested. Here, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1305
更新日期:2012-05-01 00:00:00
abstract::PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). Started at the Real World Computing Partnership (RWCP) in August 1997, it developed to the present system of PDB-REPRDB. In April 2001, the system was moved to the Computational Biology Research Center (CBRC), National Institut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg022
更新日期:2003-01-01 00:00:00
abstract::Naturally occurring RNAs are known to exhibit a high degree of modularity, whereby specific structural modules (or motifs) can be mixed and matched to create new molecular architectures. The modular nature of RNA also affords researchers the ability to characterize individual structural elements in controlled syntheti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz304
更新日期:2019-07-09 00:00:00
abstract::A role for BRCA1 in the direct and indirect regulation of transcription is well established. However, a comprehensive view of the degree to which BRCA1 impacts transcriptional regulation on a genome-wide level has not been defined. We performed genome-wide expression profiling and ChIP-chip analysis, comparison of whi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr679
更新日期:2011-12-01 00:00:00
abstract::The mutations of 76 haemophilia B patients representing the whole population registered with the Malmö haemophilia centre (42) and referrals from the UK, were characterised. RFLP haplotype analysis of the defective genes indicated that 51 single base pair substitutions were definitely of independent origin and 27 of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.11.3227
更新日期:1990-06-11 00:00:00
abstract::The sigma(54) factor associates with core RNA polymerase (RNAP) to form a holoenzyme that is unable to initiate transcription unless acted on by an activator protein. sigma(54) is closely involved in many steps of activator-dependent transcription, such as core RNAP binding, promoter recognition, activator interaction...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp419
更新日期:2009-07-01 00:00:00
abstract::We have sequenced the external transcribed spacer (ETS) of a ribosomal transcription unit from Xenopus laevis, together with sections of the preceding non-transcribed spacer. Our analysis was carried out on the same cloned transcription unit as that from which the internal transcribed spacers (ITS) were previously seq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.7.2387
更新日期:1982-04-10 00:00:00
abstract::We describe an improved model of DNA replication in Xenopus egg extracts, in which a circular plasmid immobilized on paramagnetic beads is used as a template. DNA synthesis occurred on either circular or linear plasmids coupled to the beads, but only DNA synthesis on the circular plasmid was inhibited by geminin and a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl512
更新日期:2006-07-26 00:00:00
abstract::PAX6 is a transcription factor that plays a major role in ocular morphogenesis. PAX6 is expressed in the eye, central nervous system and pancreas. Two alternative promoters, P0 and P1, which are differentially regulated during development, drive PAX6 transcription. We identified a 57 bp cis-regulatory element in exon ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.19.4070
更新日期:2001-10-01 00:00:00
abstract::Error-free lesion bypass and error-prone lesion bypass are important cellular responses to DNA damage during replication, both of which require a DNA polymerase (Pol). To identify lesion bypass DNA polymerases, we have purified human Polkappa encoded by the DINB1 gene and examined its response to damaged DNA templates...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.21.4138
更新日期:2000-11-01 00:00:00
abstract::The swi4+ gene of Schizosaccharomyces pombe is involved in termination of copy-synthesis during mating-type switching. The gene was cloned by functional complementation of a swi4 mutant transformed with a genomic library. Determination of the nucleotide sequence revealed an open reading frame of 2979 nucleotides which...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.9.2271
更新日期:1992-05-11 00:00:00
abstract::Bacteria belonging to the class Mollicutes were among the first ones to be selected for complete genome sequencing because of the minimal size of their genomes and their pathogenicity for humans and a broad range of animals and plants. At this time six genome sequences have been publicly released (Mycoplasma genitaliu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh114
更新日期:2004-01-01 00:00:00
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
更新日期:2018-05-18 00:00:00
abstract::Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt713
更新日期:2013-11-01 00:00:00
abstract::Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1245
更新日期:2019-02-20 00:00:00
abstract::In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adap...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz425
更新日期:2019-08-22 00:00:00
abstract::This article describes recent developments of Europe PMC (http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1061
更新日期:2015-01-01 00:00:00