Abstract:
:We provide a novel web service, called rQuant.web, allowing convenient access to tools for quantitative analysis of RNA sequencing data. The underlying quantitation technique rQuant is based on quadratic programming and estimates different biases induced by library preparation, sequencing and read mapping. It can tackle multiple transcripts per gene locus and is therefore particularly well suited to quantify alternative transcripts. rQuant.web is available as a tool in a Galaxy installation at http://galaxy.fml.mpg.de. Using rQuant.web is free of charge, it is open to all users, and there is no login requirement.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bohnert R,Rätsch Gdoi
10.1093/nar/gkq448subject
Has Abstractpub_date
2010-07-01 00:00:00pages
W348-51issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkq448journal_volume
38pub_type
杂志文章abstract::Toscana virus is an emerging bunyavirus in Mediterranean Europe where it accounts for 80% of pediatric meningitis cases during the summer. The negative-strand ribonucleic acid (RNA) genome of the virus is wrapped around the virally encoded nucleoprotein N to form the ribonucleoprotein complex (RNP). We determined crys...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku229
更新日期:2014-05-01 00:00:00
abstract::A comparison of gene structure, sequence, and transcription pattern of heat shock loci 93D of Drosophila melanogaster and 48B of Drosophila hydei has been performed. Both heat shock loci consist of an unique region that is flanked by an internally repetitive element. Different members of these elements are highly cons...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.8.3317
更新日期:1987-04-24 00:00:00
abstract::Strand Displacement Amplification (SDA) is an isothermal, in vitro method of amplifying a DNA target sequence prior to detection [Walker et al (1992) Nucleic Acids Res., 20, 1691-1693]. Here we describe a multiplex form of SDA that allows two target sequences and an internal amplification control to be co-amplified by...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.13.2670
更新日期:1994-07-11 00:00:00
abstract::The unknown modified nucleotide G*, isolated from both Schizosaccharomyces pombe and Torulopsis utilis initiator tRNAs(Met), has been identified as an O-ribosyl-(1"----2')-guanosine-5"-phosphate, called Gr(p), by means of HPLC, UV-absorption, mass spectrometry and periodate oxidation procedures. By comparison with the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5199
更新日期:1991-10-11 00:00:00
abstract::TFIIIC is a RNA polymerase (pol) III-specific DNA-binding factor that is required for transcription of tRNA and 5S rRNA genes. Active human TFIIIC consists of five subunits. However, an inactive form has also been isolated that lacks one of the five subunits, called TFIIIC110. A model was proposed in which pol III tra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl432
更新日期:2006-07-05 00:00:00
abstract::Stress response mechanisms that modulate the dynamics of tRNA degradation and accumulation from the cytoplasm to the nucleus have been studied in yeast, the rat hepatoma and human cells. In the current study, we investigated tRNA degradation and accumulation in HeLa cells under various forms of stress. We found that i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt153
更新日期:2013-04-01 00:00:00
abstract::Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa174
更新日期:2020-05-07 00:00:00
abstract::We have carried out a survey of potential quadruplex structure sequences (PQSS), which occur in the immediate upstream region (500 bp) of human genes. By examining the number and distribution of these we have established that there is a clear link between them and the occurrence of the SP1-binding element 'GGGCGG', su...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn078
更新日期:2008-05-01 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
abstract::The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.2.555
更新日期:1988-01-25 00:00:00
abstract::It is a central issue to elucidate the new type of molecular recognition accompanied by a global structural change of a molecule upon binding to its targets. Here we investigate the driving force for the binding of R12 (a ribonucleic acid aptamer) and P16 (a partial peptide of a prion protein) during which P16 exhibit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku382
更新日期:2014-06-01 00:00:00
abstract::We have recently described three group I introns inserted into a single gene, orf142, of the staphylococcal bacteriophage Twort and suggested the presence of at least two additional self-splicing introns in this phage genome. Here we report that two previously uncharacterized introns, 429 and 1087 nt in length, interr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.9.1935
更新日期:2002-05-01 00:00:00
abstract::The synthetic DNA fragment (formula, see text) (corresponding to nucleotides 4299-4314 of the phi X DNA sequence) was cloned into either the AmpR gene or the KmR gene of plasmid pACYC 177. The DNA sequence of the KmR gene around the insertion site was determined by nucleotide sequence analysis of the pACYC 177 FnudII ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.14.3335
更新日期:1981-07-24 00:00:00
abstract::An open reading frame upstream from nifHDK operon of Klebsiella pneumoniae had been described. The orientation of this open reading frame is opposite to that of nifHDK and sequence homology was found between the open reading frame promoter and the promoter of nifHDK operon. A recombinant plasmid carrying the promoter ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.12.4241
更新日期:1983-06-25 00:00:00
abstract::The pDd56 mRNA sequence is highly enriched in prestalk over prespore cells and is inducible by DIF, the putative Dictyostelium stalk-specific morphogen. We show that the pDd56 gene is composed of forty one copies of a twenty four amino acid, cysteine rich repeat. This is highly homologus to a repeat which we have prev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.18.7463
更新日期:1987-09-25 00:00:00
abstract::Metnase is a human protein with methylase (SET) and nuclease domains that is widely expressed, especially in proliferating tissues. Metnase promotes non-homologous end-joining (NHEJ), and knockdown causes mild hypersensitivity to ionizing radiation. Metnase also promotes plasmid and viral DNA integration, and topoisom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq339
更新日期:2010-09-01 00:00:00
abstract::Histone variants play an important role in shaping the mammalian epigenome and their aberrant expression is frequently observed in several types of cancer. However, the mechanisms that mediate their function and the composition of the variant-containing chromatin are still largely unknown. A proteomic interrogation of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku303
更新日期:2014-06-01 00:00:00
abstract::The frequency occurrences of K-tuple (overlapping sequences of defined length, K) were computed from the known human genome sequences. The significance of these frequencies for the whole human genome was tested by polymerase chain reaction (PCR). A computer programs based on these results was written to choose primers...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.14.3887
更新日期:1991-07-25 00:00:00
abstract::The specific recognition of homopurine-homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Alkylation of nucleobases with functionalized TFOs would have the potential for site-directed mutagenesis. Recently, we demonstrated that a T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng031
更新日期:2003-03-15 00:00:00
abstract::The higher order structure of the functionally important 530 loop in Escherichia coli 16S rRNA was studied in mutants with single base changes at position 517, which significantly impair translational fidelity. The 530 loop has been proposed to interact with the EF-Tu-GTP-aatRNA ternary complex during decoding. The re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.17.3563
更新日期:1995-09-11 00:00:00
abstract::Recent studies show that the region of DNA brought into close proximity to the fetal gamma-globin genes in deletional forms of hereditary persistence of fetal hemoglobin (HPFH) is selectively hypomethylated (and presumably active) in normal erythroid tissue. This region is normally located approximately 100 kilobases ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.13.5169
更新日期:1987-07-10 00:00:00
abstract::Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj058
更新日期:2006-01-01 00:00:00
abstract::Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segmen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm245
更新日期:2007-01-01 00:00:00
abstract::Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we used enha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1055
更新日期:2020-12-02 00:00:00
abstract::Rotaviruses are a major cause of acute, often fatal, gastroenteritis in infants and young children world-wide. Virions contain an 11 segment double-stranded RNA genome. Little is known about the cis-acting sequences and structural elements of the viral RNAs. Using a database of 1621 full-length sequences of mammalian ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq663
更新日期:2010-11-01 00:00:00
abstract::The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nasce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx318
更新日期:2017-07-27 00:00:00
abstract::Methylation of miRNAs at the 2'-hydroxyl group on the ribose at 3'-end (2'-O-methylation, 2'Ome) is critical for miRNA function in plants and Drosophila. Whether this methylation phenomenon exists for mammalian miRNA remains unknown. Through LC-MS/MS analysis, we discover that majority of miR-21-5p isolated from human...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa504
更新日期:2020-07-27 00:00:00
abstract::The continuing threat of infectious disease and future pandemics, coupled to the continuous increase of drug-resistant pathogens, makes the discovery of new and better vaccines imperative. For effective vaccine development, antigen discovery and validation is a prerequisite. The compilation of information concerning p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp830
更新日期:2010-01-01 00:00:00
abstract::Two CTAG-recognizing restriction and modification (R/M) systems, designated MthZI and MthFI, were identified in the thermophilic archaeon Methanobacterium thermoformicicum strains Z-245 and FTF, respectively. Further analysis revealed that the methyltransferase (MTase) genes are plasmid-located in both strains. The pl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.19.5047
更新日期:1992-10-11 00:00:00
abstract::We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks535
更新日期:2012-07-01 00:00:00