Abstract:
:Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the intron-exon arrangement of a gene is essential, usually obtained by aligning mRNA/EST sequences to their cognate genomic sequences. MGAlign is a novel, rapid, memory efficient and practical method for aligning mRNA/EST and genome sequences. We present here a freely available web service, MGAlignIt (http://origin.bic.nus.edu.sg/mgalign/mgalignit), based on MGAlign. Besides the alignment itself, this web service allows users to effectively visualize the alignment in a graphical manner and to perform limited analysis on the alignment output. The server also permits the alignment to be saved in several forms, both graphical and text, suitable for further processing and analysis by other programs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lee BT,Tan TW,Ranganathan Sdoi
10.1093/nar/gkg561keywords:
subject
Has Abstractpub_date
2003-07-01 00:00:00pages
3533-6issue
13eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments. We have processed 300 602 such clones from both public and private projects to generate 28,199 'UniTraps', i.e. distinct collections of unambiguous insertions at the same subgenic regi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm825
更新日期:2008-01-01 00:00:00
abstract::Homologous recombination (HR) is a highly accurate mechanism of DNA repair that can be exploited for homology-directed gene targeting. Since in most cell types HR occurs very infrequently (approximately 10(-6) to 10(-8)), its practical application has been largely restricted to specific experimental systems that allow...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp643
更新日期:2009-09-01 00:00:00
abstract::Prior work has indicated that an octanucleotide [5'TATAAGTA(+1)3'] sequence is used as a promoter in yeast mitochondria. Two such sequences (FP1 and FP2) are present upstream of the tRNA(fMet)-RNAse P RNA -tRNA(Pro) gene cluster but only the FP1 promoter but not the FP2 appears to be active in vivo and in vitro. The r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.21.5937
更新日期:1991-11-11 00:00:00
abstract::Expressed polycistronic microRNA (miR) cassettes have useful properties that can be utilized for RNA interference (RNAi)-based gene silencing. To advance their application we generated modular trimeric anti-hepatitis B virus (HBV) Pol II cassettes encoding primary (pri)-miR-31-derived shuttles that target three differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp446
更新日期:2009-07-01 00:00:00
abstract::In the haploid genome of Xenopus laevis there are two genes coding for the r-protein L14. It is not known if they are located on the same chromosome. cDNA clones deriving from the transcripts of the two genes have been isolated from an oocyte messenger cDNA bank showing that they are both expressed. We have studied th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.19.7633
更新日期:1986-10-10 00:00:00
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::Two dimensional (2D) NMR and molecular dynamics simulations have been used to determine the three dimensional (3D) structure of a hairpin DNA, d-CTA-GAGGATCC-TUTT-GGATCCT (22mer; abbreviated as U2-hairpin), which has uracil at the second position from the 5' end of the tetraloop. The(1)H resonances of this hairpin hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.9.1906
更新日期:2000-05-01 00:00:00
abstract::We used 2D protein gel electrophoresis and DNA microarray technologies to systematically analyze genes under glucose repression in B:acillus subtilis. In particular, we focused on genes expressed after the shift from glycolytic to gluconeogenic at the middle logarithmic phase of growth in a nutrient sporulation medium...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.3.683
更新日期:2001-02-01 00:00:00
abstract::Genes from yeast to mammals are frequently subject to non-coding transcription of their antisense strand; however the genome-wide role for antisense transcription remains elusive. As transcription influences chromatin structure, we took a genome-wide approach to assess which chromatin features are associated with nasc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv666
更新日期:2015-09-18 00:00:00
abstract::The 5'-cap of spliceosomal small nuclear RNAs, some small nucleolar RNAs and of telomerase RNA was found to be hypermethylated in vivo. The Trimethylguanosine Synthase 1 (TGS1) mediates this conversion of the 7-methylguanosine-cap to the 2,2,7-trimethylguanosine (m(3)G)-cap during maturation of the RNPs. For mammalian...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp249
更新日期:2009-07-01 00:00:00
abstract::Alternative splicing is widespread in mammalian gene expression, and variant splice patterns are often specific to different stages of development, particular tissues or a disease state. There is a need to systematically collect data on alternatively spliced exons, introns and splice isoforms, and to annotate this dat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh030
更新日期:2004-01-01 00:00:00
abstract::Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw095
更新日期:2016-06-02 00:00:00
abstract::Human Ape2 protein has 3' phosphodiesterase activity for processing 3'-damaged DNA termini, 3'-5' exonuclease activity that supports removal of mismatched nucleotides from the 3'-end of DNA, and a somewhat weak AP-endonuclease activity. However, very little is known about the role of Ape2 in DNA repair processes. Here...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp357
更新日期:2009-07-01 00:00:00
abstract::Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets ...
journal_title:Nucleic acids research
pub_type: 杂志文章,meta分析
doi:10.1093/nar/gkp093
更新日期:2009-05-01 00:00:00
abstract::Unlike short interfering RNAs (siRNAs), which are commonly designed to repress a single messenger RNA (mRNA) target through perfect base pairing, microRNAs (miRNAs) are endogenous small RNAs that have evolved to concurrently repress multiple mRNA targets through imperfect complementarity. MicroRNA target recognition i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku171
更新日期:2014-05-01 00:00:00
abstract::Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.5.1943
更新日期:1986-03-11 00:00:00
abstract::SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv351
更新日期:2015-07-01 00:00:00
abstract::The Bovine Genome Database (BGD; http://BovineGenome.org) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1235
更新日期:2011-01-01 00:00:00
abstract::Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, her...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx407
更新日期:2017-07-03 00:00:00
abstract::The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.13.2576
更新日期:1994-07-11 00:00:00
abstract::The remarkable selectivity of N-methyl mesoporphyrin IX (NMM) for G-quadruplexes (GQs) is long known, however its ability to stabilize and bind GQs has not been investigated in detail. Through the use of circular dichroism, UV-visible spectroscopy and fluorescence resonance energy transfer (FRET) melting assay we have...
journal_title:Nucleic acids research
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更新日期:2012-07-01 00:00:00
abstract::DNA restriction fragments located 5' to the human c-myc gene display anomalous electrophoretic mobility on polyacrylamide gels. Computer modeling of the c-myc flanking DNA suggests that the slow-moving DNA fragments spanning nucleotides -1690 to -1054 (relative to c-myc promoter P1) and -718 to -452 form large left ha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.7.2819
更新日期:1989-04-11 00:00:00
abstract::The transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas9) utlilize distinct molecular mechanisms in targeting site recognition. The two proteins can be modified to carry additional functional domains to regulate exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku836
更新日期:2014-11-10 00:00:00
abstract::The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1025
更新日期:2021-01-08 00:00:00
abstract::Phosphorylation of the easily accessible 3',5'-diesters 1a-d with diphenyl phosphorochloridate, followed by selective 5'-deacylation, affords the phosphotriester derivatives 2a-d in good yields. Alkaline treatment of 2a-d results in the formation of the 2',3'-cyclic phosphates (3a-d). The usefulness of the phosphotrie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.10.2731
更新日期:1976-10-01 00:00:00
abstract::The design and synthesis of metal complexes that can specifically target DNA secondary structure has attracted considerable attention. Chiral metallosupramolecular complexes (e.g. helicates) in particular display unique DNA-binding behavior, however until recently few examples which are both water-compatible and enant...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx244
更新日期:2017-05-19 00:00:00
abstract::The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.23.9861
更新日期:1987-12-10 00:00:00
abstract::Transcription factor binding sites (TFBSs) are short DNA sequences interacting with transcription factors (TFs), which regulate gene expression. Due to the relatively short length of such binding sites, it is largely unclear how the specificity of protein-DNA interaction is achieved. Here, we have performed a genome-w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl248
更新日期:2006-05-02 00:00:00
abstract::TERC is an RNA component of telomerase. However, TERC is also ubiquitously expressed in most human terminally differentiated cells, which don't have telomerase activity. The function of TERC in these cells is largely unknown. Here, we report that TERC enhances the expression and secretion of inflammatory cytokines by ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz584
更新日期:2019-09-05 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