Abstract:
:Fast viral adaptation and the implication of this rapid evolution in the emergence of several new infectious diseases have turned this issue into a major challenge for various research domains. Indeed, viruses are involved in the development of a wide range of pathologies and understanding how viruses and host cells interact in the context of adaptation remains an open question. In order to provide insights into the complex interactions between viruses and their host organisms and namely in the acquisition of novel functions through exchanges of genetic material, we developed the PhEVER database. This database aims at providing accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. PhEVER (http://pbil.univ-lyon1.fr/databases/phever) is a unique database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. PhEVER integrates extensive data from up-to-date completely sequenced genomes (2426 non-redundant viral genomes, 1007 non-redundant prokaryotic genomes, 43 eukaryotic genomes ranging from plants to vertebrates) and offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families. Public access to PhEVER is available through its webpage and through all dedicated ACNUC retrieval systems.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Palmeira L,Penel S,Lotteau V,Rabourdin-Combe C,Gautier Cdoi
10.1093/nar/gkq1013subject
Has Abstractpub_date
2011-01-01 00:00:00pages
D569-75issue
Database issueeissn
0305-1048issn
1362-4962pii
gkq1013journal_volume
39pub_type
杂志文章abstract::PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1359
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journal_title:Nucleic acids research
pub_type: 杂志文章,多中心研究
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abstract::Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2723
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journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3'UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkp078
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abstract::The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association ...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkh236
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abstract::The cold shock domain is one of the most highly conserved motifs between bacteria and higher eukaryotes. Y-box-binding proteins represent a subfamily of cold shock domain proteins with pleiotropic functions, ranging from transcription in the nucleus to translation in the cytoplasm. These proteins have been investigate...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1077
更新日期:2014-12-01 00:00:00
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journal_title:Nucleic acids research
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abstract::Mutant AraC proteins were selected for their ability to induce but not to repress, or their ability to repress but not to induce the araBAD operon. One such unusual mutant is able to bind to the araI site with an affinity only two to three-fold weaker than the wild type AraC protein, but the mutant protein was shown, ...
journal_title:Nucleic acids research
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abstract::Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the program...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx638
更新日期:2017-09-19 00:00:00
abstract::In order to facilitate the direct computation of the sizes of DNA fragments separated by gel electrophoresis, we have written and evaluated programmes for the Hewlett-Packard 41C programmable calculator. The sizes estimated for DNA fragments of known length using some of these programmes were found to be more accurate...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part2.845
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abstract::The satellite RNA of tobacco ringspot virus (STobRV RNA) replicates and becomes encapsidated in association with tobacco ringspot virus. Previous results show that the infected tissue produces multimeric STobRV RNAs of both polarities. RNA that is complementary to encapsidated STobRV RNA, designated as having the (-) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.24.9729
更新日期:1986-12-22 00:00:00
abstract::The long interspersed repeated DNA family of rats (LINE or L1Rn family) contains about 40,000 6.7-kilobase (kb) long members (1). LINE members may be currently mobile since their presence or absence causes allelic variation at three single copy loci (2, 3): insulin 1, Moloney leukemia virus integration 2 (Mlvi-2) (4),...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.9.3717
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abstract::The cyanobacteirum Synechocystis sp. strain PCC 6803 possesses nine species of the sigma (sigma)-factor gene for RNA polymerase (RNAP). Here, we identify and characterize the novel-type promoter recognized by a group 3 sigma-factor, SigF. SigF autoregulates its own transcription and recognizes the promoter of pilA1 th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn453
更新日期:2008-09-01 00:00:00
abstract::We report the isolation of a novel human POU domain encoding gene named RDC-1. The POU domain of the RDC-1 encoded protein is highly related to the POU domain potentially encoded by the rat brain-3 sequence and to that of the Drosophila I-POU protein; outside of the POU region, RDC-1 is unrelated to any previously cha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.18.4919
更新日期:1992-09-25 00:00:00
abstract::Expression of a proof-reading deficient form of mitochondrial DNA (mtDNA) polymerase gamma, POLG, causes early death accompanied by features of premature ageing in mouse. However, the mechanism of cellular senescence remains unresolved. In addition to high levels of point mutations of mtDNA, the POLG mutator mouse har...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp091
更新日期:2009-04-01 00:00:00
abstract::Transcription of 5S RNA gene in Xenopus oocytes requires a 38 kDa transcription factor TFIIIA, which interacts with the 50 bp internal control region of the gene. We looked for TFIIIA-like polypeptides in the extracts of adult Xenopus tissues on the basis of their antigenic cross-reactivity to anti-TFIIIA antibody. Se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.14.5597
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki682
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abstract::While antibiotic selection has been routinely used for the selection of genetically modified cells, administration of cytotoxic drugs often leads to deleterious effects not only to inert cells but also to transfected or transduced ones. In this study, we propose an Antigen-MEdiated Genetically modified cell Amplificat...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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abstract::Translation Initiator of Short 5' UTR (TISU) is a unique regulatory element of both transcription and translation initiation. It is present in a sizable number of genes with basic cellular functions and a very short untranslated region (5' UTR). Here, we investigated translation initiation from short 5' UTR mRNAs with...
journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::We have investigated the response of the filamentous fungus Aspergillus nidulans to low, non-killing, doses of the alkylating agent MNNG (N-methyl-N'-nitro-N-nitrosoguanidine). Such treatment causes a substantial induction of DNA alkyltransferase activity, with the specific activity in treated cells increasing up to o...
journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemente...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1111
更新日期:2016-02-29 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::Fibroblast growth factor receptor 3 (FGFR3) plays an important role in cartilage development. Although upregulation of FGFR3 expression in response to bone morphogenetic protein-2 (BMP-2) has been reported, the molecular mechanisms remain unknown. In this study, we used in vivo approaches to characterize BMP-2-induced...
journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz344
更新日期:2019-07-09 00:00:00
abstract::Yeast two-hybrid (Y2H) screenings result in identification of many out-of-frame (OOF) clones that code for short (2-100 amino acids) peptides with no sequence homology to known proteins. We hypothesize that these peptides can reveal common short linear motifs (SLiMs) responsible for their selection. We present a new p...
journal_title:Nucleic acids research
pub_type: 杂志文章
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