Abstract:
:Mitome is a specialized mitochondrial genome database designed for easy comparative analysis of various features of metazoan mitochondrial genomes such as base frequency, A+T skew, codon usage and gene arrangement pattern. A particular function of the database is the automatic reconstruction of phylogenetic relationships among metazoans selected by a user from a taxonomic tree menu based on nucleotide sequences, amino acid sequences or gene arrangement patterns. Mitome also enables us (i) to easily find the taxonomic positions of organisms of which complete mitochondrial genome sequences are publicly available; (ii) to acquire various metazoan mitochondrial genome characteristics through a graphical genome browser; (iii) to search for homology patterns in mitochondrial gene arrangements; (iv) to download nucleotide or amino acid sequences not only of an entire mitochondrial genome but also of each component; and (v) to find interesting references easily through links with PubMed. In order to provide users with a dynamic, responsive, interactive and faster web database, Mitome is constructed using two recently highlighted techniques, Ajax (Asynchronous JavaScript and XML) and Web Services. Mitome has the potential to become very useful in the fields of molecular phylogenetics and evolution and comparative organelle genomics. The database is available at: http://www.mitome.info.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lee YS,Oh J,Kim YU,Kim N,Yang S,Hwang UWdoi
10.1093/nar/gkm763subject
Has Abstractpub_date
2008-01-01 00:00:00pages
D938-42issue
Database issueeissn
0305-1048issn
1362-4962pii
gkm763journal_volume
36pub_type
杂志文章abstract::The repetitive fraction of the genome of the eukaryotic slime mould Physarum polycephalum is dominated by the Tp1 family of highly repetitive retrotransposon-like sequences. Tp1 elements consist of two terminal direct repeats of 277bp which flank an internal domain of 8.3kb. They are the major sequence component in th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.2.279
更新日期:1991-01-25 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::Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5' mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a mino...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz681
更新日期:2019-09-26 00:00:00
abstract::The DNA-binding protein RdgC has been identified as an inhibitor of RecA-mediated homologous recombination in Escherichia coli. In Neisseria species, RdgC also has a role in virulence-associated antigenic variation. We have previously solved the crystal structure of the E. coli RdgC protein and shown it to form a toro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq509
更新日期:2010-10-01 00:00:00
abstract::Two DNA hexadecamers containing one central 5'-GC-3' base step have been examined by footprinting methodology in the presence and absence of actinomycin D. The results of these studies, coupled with imino proton NMR measurements indicate that the antitumor drug causes a change in DNA conformation at a distance from th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.23.11125
更新日期:1988-12-09 00:00:00
abstract::A positive cis-acting DNA element in the near 5'-upstream region of the CYP2B1/B2 genes in rat liver was found to play an important role in the transcription of these genes. An oligonucleotide covering -69 to -98 nt mimicked the gel mobility shift pattern given by the fragment -179 to +29 nt, which was earlier found a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.3.557
更新日期:1992-02-11 00:00:00
abstract::We have isolated from a single human liver cDNA library two clones which are highly homologous (78% over the coding region) to the major phenobarbital-inducible P450 from rat (P450IIB1). This is the first direct demonstration of the presence of the P450IIB gene subfamily in humans. This subfamily is much less extensiv...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.13.5783
更新日期:1988-07-11 00:00:00
abstract::In eukaryotes, exposure to stress conditions causes a shift from cap-dependent to cap-independent translation. In trypanosomatids, environmental switches are the driving force of a developmental program of gene expression, but it is yet unclear how their translation machinery copes with their constantly changing envir...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr555
更新日期:2011-10-01 00:00:00
abstract::Human telomerase is a ribonucleoprotein which uses its internal RNA moiety as a template for telomeric DNA synthesis. This enzyme is up-regulated in most malignant tumors and is therefore considered as a possible cancer target. Here we examined the effects of differently modified oligomers on telomeraseactivity from H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.4.1152
更新日期:1999-02-15 00:00:00
abstract::Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku463
更新日期:2014-07-01 00:00:00
abstract::Evidence will be presented to show that the allyl group is suitable for the protection of a 3'-terminal phosphodiester function. The latter will be demonstrated by the synthesis, via a phosphotriester approach, of two cyclic tetraribonucleotides [r(AAAA) and r(UAMe2UAMe2)], two cyclic hexadeoxyribonucleotides [d(CGCGC...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4607
更新日期:1988-05-25 00:00:00
abstract::Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na+ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na+ a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw845
更新日期:2016-12-01 00:00:00
abstract::Synthesis and radioiodination of a stannyl oligodeoxyribonucleotide were undertaken to evaluate a gamma ray emitting ODN ligand for thrombus imaging in vivo . Synthesis of the ODN was based on modified automatedbeta-cyanoethyl phosphoramidite chemistry with an organotin nucleoside (dU*) coupled to a thrombin binding a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.14.2897
更新日期:1997-07-15 00:00:00
abstract::The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1124
更新日期:2008-03-01 00:00:00
abstract::Intron retention (IR) has been proposed to modulate the delay between transcription and translation. Here, we provide an exhaustive characterization of IR in differentiated white blood cells from both the myeloid and lymphoid lineage where we observed highest levels of IR in monocytes and B-cells, in addition to previ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1180
更新日期:2020-02-20 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::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::An oligodeoxyribonucleotide, d(GCTCACAAT-X-ATTGTGAGC), where X represents a hexaethylene glycol chain, was studied using circular dichroism spectroscopy. Its conformation and conformational stability were compared to those of compounds where X was replaced by four thymines and to the duplex of same sequence without lo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.21.6353
更新日期:1990-11-11 00:00:00
abstract::Silencing gene expression by siRNAs is rapidly becoming a powerful tool for the genetic analysis of mammalian cells. However, the rapid degradation of siRNA and the limited duration of its action call for an efficient delivery technology. Accordingly, we describe here that Atelocollagen complexed with siRNA is resista...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh093
更新日期:2004-07-22 00:00:00
abstract::The molecular mechanism in pancreatic β cells underlying hyperlipidemia and insulin insufficiency remains unclear. Here, we find that the fatty acid-induced decrease in insulin levels occurs due to a decrease in insulin translation. Since regulation at the translational level is generally mediated through RNA-binding ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky867
更新日期:2018-12-14 00:00:00
abstract::A novel cytoplasmic gene expression system has been developed. This system differs from other expression systems in that it relies on the co-delivery of plasmid DNA and T7 RNA polymerase (RNAP) during transfection. The plasmid contains a T7 RNAP gene driven by the T7 promoter (T7 autogene) and a functional/reporter ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.11.2114
更新日期:1994-06-11 00:00:00
abstract::Work from a number of laboratories has indicated that the TATA box sequence can act as a basal promoter element not only for RNA polymerase II (RNAP II) transcription, but also for transcription by RNA polymerase III (RNAP III). We previously reported that, in the absence of other cis-acting elements, the canonical TA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.15.3100
更新日期:1996-08-01 00:00:00
abstract::The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problema...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa980
更新日期:2021-01-08 00:00:00
abstract::Histone H2A ubiquitination plays critical roles in transcriptional repression and deoxyribonucleic acid (DNA) damage response. More attention has been focused on ubiquitin E3 ligases of H2A, however, less is known about the negative regulators of H2A ubiquitination. Here we identified HSCARG as a new negative regulato...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku230
更新日期:2014-05-01 00:00:00
abstract::To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl781
更新日期:2007-01-01 00:00:00
abstract::Many enzymes acting on DNA require Mg(2+) ions not only for catalysis but also to bind DNA. Binding studies often employ Ca(2+) as a substitute for Mg(2+), to promote DNA binding whilst disallowing catalysis. The SfiI endonuclease requires divalent metal ions to bind DNA but, in contrast to many systems where Ca(2+) m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp569
更新日期:2009-09-01 00:00:00
abstract::Alternative splicing is the primary source of proteome complexity in metazoans and its regulation shapes the proteome in response to shifting physiological requirements. We developed a bichromatic splicing reporter that uses a peculiar feature of some fluorescent protein coding regions to express two different fluores...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl967
更新日期:2006-01-01 00:00:00
abstract::Minigenes encoding the peptide Met-Arg-Arg have been used to study the mechanism of toxicity of AGA codons proximal to the start codon or prior to the termination codon in bacteria. The codon sequences of the 'mini-ORFs' employed were initiator, combinations of AGA and CGA, and terminator. Both, AGA and CGA are low-us...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh784
更新日期:2004-08-18 00:00:00
abstract::The PriA protein was identified in Escherichia coli as a factor involved in the replication of extrachromosomal elements such as bacteriophage phiX174 and plasmid pBR322. Recent data show that PriA plays an important role in chromosomal replication, by promoting reassembly of the replication machinery during reinitiat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.7.1593
更新日期:2002-04-01 00:00:00
abstract::Reactive oxygen species (ROS) have been implicated as the cause of cumulative damage to DNA, proteins and lipids that can ultimately result in cell death. A common problem when measuring oxidative DNA damage has been the introduction of modifications in the native state of the molecule by many DNA isolation methods. W...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.4.968
更新日期:2000-02-15 00:00:00