Abstract:
:Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 complete genome sequences. The data provide the first glimpses of conservation of multiple ncRNA families across a wide taxonomic range. A small number of large families are essential in all three kingdoms of life, with large numbers of smaller families specific to certain taxa. Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Griffiths-Jones S,Moxon S,Marshall M,Khanna A,Eddy SR,Bateman Adoi
10.1093/nar/gki081keywords:
subject
Has Abstractpub_date
2005-01-01 00:00:00pages
D121-4issue
Database issueeissn
0305-1048issn
1362-4962pii
33/suppl_1/D121journal_volume
33pub_type
杂志文章abstract::The primary structure of the E. coli rpoC gene (5321 base pairs) coding the beta'-subunit of RNA polymerase as well as its adjacent segment have been determined. The structure analysis of the peptides obtained by cleavage of the protein with cyanogen bromide and trypsin has confirmed the amino acid sequence of the bet...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.13.4035
更新日期:1982-07-10 00:00:00
abstract::The binding of nine aminoalkyl adenylates to isoleucyl-tRNA synthetase from Escherichia coli MRE 600 was measured and compared with the binding of the cognate amino acids. It was found that they bind rather tightly to the enzyme, the Kd's ranging from 3.1.10(-4) M with glycinol-AMP ester to 3.7.10(-9) M with L-isoleuc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.3.673
更新日期:1977-03-01 00:00:00
abstract::During DNA double-strand break and replication fork repair by homologous recombination, the RAD51 recombinase catalyzes the DNA strand exchange reaction via a helical polymer assembled on single-stranded DNA, termed the presynaptic filament. Our published work has demonstrated a dual function of the SWI5-SFR1 complex ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw375
更新日期:2016-07-27 00:00:00
abstract::The A site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting 'off' state and an active decoding 'on' state. Eight crystal structures of RNA duplexes containing two minimal decoding A sites of the Homo sapiens mitochondrial wild-type, the A1555G mutant or...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn112
更新日期:2008-05-01 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
pub_type: 杂志文章,评审
doi:10.1093/nar/gkw608
更新日期:2016-09-30 00:00:00
abstract::The nucleotide sequences of eight partial and five full-length phaseolin cDNA clones show that phaseolin polypeptides are encoded by two distinct gene families which differ in their coding regions by the presence or absence of two different size direct repeats. The alpha-type phaseolin polypeptides are encoded by gene...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.18.6483
更新日期:1985-09-25 00:00:00
abstract::Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an addi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr054
更新日期:2011-06-01 00:00:00
abstract::Much effort has long been devoted to unraveling the coordinated cellular response to genotoxic insults. In view of the difficulty of obtaining human biological samples of homogeneous origin, I have established a set of stable human clones where one DNA repair gene has been stably silenced by means of RNA interference....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm195
更新日期:2007-01-01 00:00:00
abstract::Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku677
更新日期:2014-10-01 00:00:00
abstract::Human apolipoprotein (apo) B mRNA is edited in a tissue specific reaction, to convert glutamine codon 2153 (CAA) to a stop translation codon. The RNA editing product templates and hybridises as uridine, but the chemical nature of this reaction and the physical identity of the product are unknown. After editing in vitr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.6.1197
更新日期:1991-03-25 00:00:00
abstract::Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom availa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky033
更新日期:2018-03-16 00:00:00
abstract::Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1165
更新日期:2015-01-01 00:00:00
abstract::We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.18.3433
更新日期:2000-09-15 00:00:00
abstract::PRINTS is a database of protein family 'fingerprints' offering a diagnostic resource for newly-determined sequences. By contrast with PROSITE, which uses single consensus expressions to characterise particular families, PRINTS exploits groups of motifs to build characteristic signatures. These signatures offer improve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.304
更新日期:1998-01-01 00:00:00
abstract::MicroRNA 26a (miR-26a) reduces cell viability in several cancers, indicating that miR-26a could be used as a therapeutic option in patients. We demonstrate that miR-26a not only inhibits G1-S cell cycle transition and promotes apoptosis, as previously described, but also regulates multiple cell cycle checkpoints. We s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx022
更新日期:2017-05-05 00:00:00
abstract::In the fission yeast Schizosaccharomyces pombe, the cdc11 gene is required for the initiation of septum formation at the end of mitosis. The sce3 gene was cloned as a multi-copy suppressor of the heat-sensitive mutant cdc11-136. When over-expressed, it rescues all mutants of cdc11 and also a heat-sensitive allele of c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.17.3433
更新日期:1997-09-01 00:00:00
abstract::We have studied the effects of the nucleotide analogue, 2',3'-dideoxythymidine-5'-triphosphate (ddTTP) on replicative DNA synthesis in HeLa cell lysates. As previously demonstrated (1), such lysates carry out extensive DNA synthesis in vitro, at rates and in a fashion similar to in vivo DNA replication. We report here...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.6.1933
更新日期:1978-06-01 00:00:00
abstract::SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm407
更新日期:2007-07-01 00:00:00
abstract::SynergyFinder (https://synergyfinder.fimm.fi) is a stand-alone web-application for interactive analysis and visualization of drug combination screening data. Since its first release in 2017, SynergyFinder has become a widely used web-tool both for the discovery of novel synergistic drug combinations in pre-clinical mo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa216
更新日期:2020-07-02 00:00:00
abstract::Prokaryotes evolved numerous systems that defend against predation by bacteriophages. In addition to well-known restriction-modification and CRISPR-Cas immunity systems, many poorly characterized systems exist. One class of such systems, named BREX, consists of a putative phosphatase, a methyltransferase and four othe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1125
更新日期:2019-01-10 00:00:00
abstract::A series of unusual folding regions (UFR) immediately 3' to the cleavage site of the outer membrane protein (OMP) and transmembrane protein (TMP) were detected in the envelope gene RNA of the human immunodeficiency virus (HIV-1, HIV-2) and simian immunodeficiency virus (SIV) by an extensive Monte Carlo simulation. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.6.1613
更新日期:1990-03-25 00:00:00
abstract::Defects in the posttranscriptional modifications of mitochondrial tRNAs have been linked to human diseases, but their pathophysiology remains elusive. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAIle 4295A>G mutation affecting a highly conserved adenosine at position 37,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1225
更新日期:2021-01-25 00:00:00
abstract::Bacterial small regulatory RNAs (sRNAs) play a major role in the regulation of various cellular functions. Most sRNAs interact with mRNA targets via an antisense mechanism, modifying their translation and/or degradation. Despite considerable progresses in discovering sRNAs in Gram-positive bacteria, their functions, f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx190
更新日期:2017-05-05 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
pub_type: 杂志文章
doi:10.1093/nar/gni059
更新日期:2005-03-30 00:00:00
abstract::Characterization of the ability of human interferons (IFNs) to rapidly induce genes led to the identification of the first two members of the STAT (signal transducers and activators of transcription) family, Stat1 and Stat2. To study the unique role of this transcription factor in IFN signaling under more physiologica...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.21.4191
更新日期:1999-11-01 00:00:00
abstract::A novel class of RNA-binding proteins, Puf, regulates translation and RNA stability by binding to specific sequences in the 3'-untranslated region of target mRNAs. Members of this protein family share a conserved Puf domain consisting of eight 36 amino acid imperfect repeats. Here we report two Puf family member genes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf600
更新日期:2002-11-01 00:00:00
abstract::With the recent increase in the number of mammalian genomes being sequenced, large-scale genome scans for human-specific positive selection are now possible. Selection can be inferred through phylogenetic analysis by comparing the rates of silent and replacement substitution between related species. Maximum-likelihood...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm764
更新日期:2008-01-01 00:00:00
abstract::An investigation of the mobility of short duplexes of DNA -octamers and decamers-on polyacrylamide gels is presented, showing that molecules containing less than one helical turn exhibit sequence dependent mobilities. Analysis of chains with different sequences indicates that any arrangement of two or more adjacent A....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.14.6803
更新日期:1988-07-25 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::YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous sequences, combined with a flexible hit criterion used to identify groups of seeds that are likely to exhibit significant ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki478
更新日期:2005-07-01 00:00:00