Abstract：
:Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
van Heel AJ,de Jong A,Song C,Viel JH,Kok J,Kuipers OPdoi
10.1093/nar/gky383subject
Has Abstractpub_date
2018-07-02 00:00:00pages
W278-W281issue
W1eissn
0305-1048issn
1362-4962pii
5000017journal_volume
46pub_type
杂志文章abstract：:Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx017
更新日期：2017-05-19 00:00:00
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：:PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.22.10669
更新日期：1988-11-25 00:00:00
abstract：:A new method of representing DNA sequences has been devised which is termed stave projection. Compared with other formats for showing the base sequences of DNA, this method greatly enhances the ease of visual analysis of the sequences of bases and it is also in a machine readable form. Using this method it is possible...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.1.509
更新日期：1986-01-10 00:00:00
abstract：:The TWIST1 bHLH transcription factor controls embryonic development and cancer processes. Although molecular and genetic analyses have provided a wealth of data on the role of bHLH transcription factors, very little is known on the molecular mechanisms underlying their binding affinity to the E-box sequence of the pro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw334
更新日期：2016-06-20 00:00:00
abstract：:Conditional gene targeting depends on tissue and time specificity of recombination events. Endogenous promoters are often used to drive various transgenic constructs. To avoid the problems associated with reconstituting a specific expression pattern in transgenic animals by this method, we tested the internal ribosome...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.6.1552
更新日期：1999-03-15 00:00:00
abstract：:Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz043
更新日期：2019-04-08 00:00:00
abstract：:Understanding networks of protein-protein interactions constitutes an essential component on a path towards comprehensive description of cell function. Whereas efficient techniques are readily available for the initial identification of interacting protein partners, practical strategies are lacking for the subsequent ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm563
更新日期：2007-01-01 00:00:00
abstract：:We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky019
更新日期：2018-04-20 00:00:00
abstract：:Slime mold, plant and insect dihydropyrimidine amidohydrolases (DHPases, EC 3.5.2.2), which catalyze the second step of pyrimidine and several anti-cancer drug degradations, were cloned and shown to functionally replace a defective DHPase enzyme in the yeast Saccharomyces kluyveri. The yeast and slime mold DHPases wer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg258
更新日期：2003-03-15 00:00:00
abstract：:Here we compare several methods for predicting oligonucleotide frequencies in 691 kb of Drosophila melanogaster DNA. As in previous work on Escherichia coli and Saccharomyces cerevisiae, a relatively simple equation based on tetranucleotide frequencies can be used in predicting frequencies of higher order oligonucleot...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.14.3651
更新日期：1992-07-25 00:00:00
abstract：:P53-binding protein 1 (53BP1) mediates DNA repair pathway choice and promotes checkpoint activation. Chromatin marks induced by DNA double-strand breaks and recognized by 53BP1 enable focal accumulation of this multifunctional repair factor at damaged chromatin. Here, we unveil an additional level of regulation of 53B...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz138
更新日期：2019-04-08 00:00:00
abstract：:Circular dichroism in the 300-360 nm region and fluorescence induced by intercaltating binding of ethidum bromide to both DNA and RNA components were studied in isolated HeLa nucleoli. Both DNA and RNA compoents contribute to the induced dichroic elliticity. Digestion of nucleoli by RNase or DNase shows that most of t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.8.1857
更新日期：1976-08-01 00:00:00
abstract：:Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp347
更新日期：2009-07-01 00:00:00
abstract：:We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. D...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg571
更新日期：2003-07-01 00:00:00
abstract：:Histone post-translational modifications have been shown to contribute to DNA damage repair. Prior studies have suggested that specific H3K79 methylation states play distinct roles in the response to UV-induced DNA damage. To evaluate these observations, we examined the effect of altered H3K79 methylation patterns on ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku242
更新日期：2014-06-01 00:00:00
abstract：:DNA methylation plays an important role in many biological processes. Existing epigenome-wide association studies (EWAS) have successfully identified aberrantly methylated genes in many diseases and disorders with most studies focusing on analysing methylation sites one at a time. Incorporating prior biological inform...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw546
更新日期：2016-09-19 00:00:00
abstract：:MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1239
更新日期：2011-04-01 00:00:00
abstract：:We recently compared the efficiency of six picornaviral internal ribosome entry segments (IRESes) and the hepatitis C virus (HCV) IRES for their ability to drive internal initiation of translationin vitro. Here we present the results of a similar comparison performed in six different cultured cell lines infected with ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.5.925
更新日期：1997-03-01 00:00:00
abstract：:Soil salinity is a significant threat to sustainable agricultural production worldwide. Plants must adjust their developmental and physiological processes to cope with salt stress. Although the capacity for adaptation ultimately depends on the genome, the exceptional versatility in gene regulation provided by the spli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1229
更新日期：2018-02-28 00:00:00
abstract：:One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm093
更新日期：2007-01-01 00:00:00
abstract：:The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.1.55
更新日期：1999-01-01 00:00:00
abstract：:R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the Reactome and KEGG databases. R spider implements a network-based statistical framework, which provides a global understanding of gene relations in the supplied ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq482
更新日期：2010-07-01 00:00:00
abstract：:The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparativ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp751
更新日期：2010-01-01 00:00:00
abstract：:Extreme overloading of HPLC columns with sample can create a condition of binding site saturation causing competition and displacement among solutes during column elution. This has been termed solute-displacement chromatography (SD-HPLC). We present an example of this phenomenon for the preparative fractionation and p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.12.2913
更新日期：1993-06-25 00:00:00
abstract：:Sae2 cooperates with the Mre11-Rad50-Xrs2 (MRX) complex to initiate resection of DNA double-strand breaks (DSBs) and to maintain the DSB ends in close proximity to allow their repair. How these diverse MRX-Sae2 functions contribute to DNA damage resistance is not known. Here, we describe mre11 alleles that suppress th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky086
更新日期：2018-04-06 00:00:00
abstract：:DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku613
更新日期：2014-01-01 00:00:00
abstract：:Melting of DNA in a segment bounded at both ends by regions of greater stability during electrophoresis in denaturing gradient gels show complex properties, not accommodated with standard melting theory. Compact bands of some DNA molecules become anomalously broadened at the retardation level in a denaturing gradient,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.14.2775
更新日期：1995-07-25 00:00:00
abstract：:A mutant at the carboxyl end of the terminal protein, p3, of phage phi 29 DNA has been constructed by inserting an containing the stop translation codon TGA in the three possible reading frames, immediately downstream of a phage phi 29 DNA fragment coding for all but the last five amino acids of protein p3. The activ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.21.7397
更新日期：1983-11-11 00:00:00
abstract：:The discoidin proteins of Dictyostelium discoideum are highly expressed during development. The Disc I gamma promoter allows the regulation of heterologous protein expression by experimental conditions. We report conditions under which the promoter activity is efficiently repressed during growth in the wildtype strain...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.6.1397
更新日期：1993-03-25 00:00:00
