Abstract:
:The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold increase in the last three years. The increase is particularly substantial for data derived from human sources. Following user requests, we added the functionality to download these tracks in bigWig format. We also incorporated new types of data (e.g. TCP-seq) as well as auxiliary tracks from other sources that help with the interpretation of Ribo-seq data. Improvements in the visualization of the data have been carried out particularly for bacterial genomes where the Ribo-seq data are now shown in a strand specific manner. For higher eukaryotic datasets, we provide characteristics of individual datasets using the RUST program which includes the triplet periodicity, sequencing biases and relative inferred A-site dwell times. This information can be used for assessing the quality of Ribo-seq datasets. To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Michel AM,Kiniry SJ,O'Connor PBF,Mullan JP,Baranov PVdoi
10.1093/nar/gkx790subject
Has Abstractpub_date
2018-01-04 00:00:00pages
D823-D830issue
D1eissn
0305-1048issn
1362-4962pii
4103596journal_volume
46pub_type
杂志文章abstract::RNA-based therapeutics, i.e. the utilization of synthetic RNA molecules to alter cellular functions, have the potential to address targets which are currently out of scope for traditional drug design pipelines. This potential however hinges on the ability to selectively deliver and internalize therapeutic RNAs into ce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky577
更新日期:2018-09-19 00:00:00
abstract::Plastid mRNA stability is tightly regulated by external signals such as light. We have investigated the biochemical mechanism responsible for the dark-induced decrease of relative half-lives for mRNAs encoding photosynthetic proteins. Protein fractions isolated from plastids of light-grown and dark-adapted plants corr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf561
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abstract::Alpha-1-microglobulin and bikunin are two plasma glycoproteins encoded by an alpha-1-microglobulin/bikunin precursor (AMBP) gene. The strict liver-specific expression of the AMBP gene is controlled by a potent enhancer made of six clustered boxes numbered 1-6 that have been reported to be proven or potential binding s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.395
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh104
更新日期:2004-07-16 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::The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1280
更新日期:2014-03-01 00:00:00
abstract::Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD+). The second domain which comprises t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1029
更新日期:2020-12-02 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz900
更新日期:2019-12-02 00:00:00
abstract::Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt718
更新日期:2013-11-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky948
更新日期:2019-01-08 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.20.7169
更新日期:1983-10-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.24.6213
更新日期:1980-12-20 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.4.671
更新日期:1992-02-25 00:00:00
abstract::The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg017
更新日期:2003-01-01 00:00:00
abstract::The vertebrate genome is a mosaic of regions differing dramatically in their G + C content. Those regions with a high G + C content contain the expected number of CpG dinucleotides and we propose that following methylation these have been protected from deamination by the increased stability of the surrounding DNA dup...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.14.5869
更新日期:1984-07-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt423
更新日期:2013-08-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.4.999
更新日期:1993-02-25 00:00:00
abstract::Engineered nucleases, which incise the genome at predetermined sites, have a number of laboratory and clinical applications. There is, however, a need for better methods for controlled intracellular delivery of nucleases. Here, we demonstrate a method for ligand-mediated delivery of zinc finger nucleases (ZFN) protein...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt710
更新日期:2013-10-01 00:00:00
abstract::Short oligo(deoxynucleoside phosphorothioate)s were analyzed as a pool of individual diastereomeric species. The composition of such mixtures, determined by means of HPLC, indicates that consecutive couplings in commonly used phosphoramidite chemistry lead to increasing contents of the Rp isomer. Methods of analysis a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.530
更新日期:1995-02-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.18.7237
更新日期:1986-09-25 00:00:00
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journal_title:Nucleic acids research
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更新日期:2011-03-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.5.1799
更新日期:1988-03-11 00:00:00
abstract::The centromere complex is a multicomponent structure essential for faithful chromosome transmission. Here we show that the S. cerevisiae centromere protein Cpf1 bends centromere DNA element I (CDEI) with the bend angle ranging from 66 degrees to 71 degrees. CDEI DNA sequences that carry point mutations which lead to r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.20.4726
更新日期:1993-10-11 00:00:00
abstract::GenBank (R) is a comprehensive sequence database that contains publicly available DNA sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg057
更新日期:2003-01-01 00:00:00
abstract::We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar struc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa629
更新日期:2020-09-04 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz973
更新日期:2020-01-08 00:00:00
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journal_title:Nucleic acids research
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doi:10.1093/nar/gks451
更新日期:2012-08-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.9.2103
更新日期:1993-05-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.3.854
更新日期:1998-02-01 00:00:00