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ReadXplorer—visualization and analysis of mapped sequences
2014
Bioinformatics
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Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data. Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions
doi:10.1093/bioinformatics/btu205
pmid:24790157
pmcid:PMC4217279
fatcat:i6o7gvzc7zbmvn4cg3nbnwlvke
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... nd displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion-insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets. Availability and implementation: ReadXplorer is available as opensource software at http://www.readxplorer.org along with a detailed manual.
EDGAR: A software framework for the comparative analysis of prokaryotic genomes
2009
BMC Bioinformatics
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The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. Results: To support these studies EDGAR -"Efficient Database framework for
doi:10.1186/1471-2105-10-154
pmid:19457249
pmcid:PMC2696450
fatcat:wk2r5gvhufginazad346jk4vxu
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... tive Genome Analyses using BLAST score Ratios" -was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. Conclusion: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http:/ /edgar.cebitec.uni-bielefeld.de, where the precomputed data sets can be browsed.
Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering
2011
Journal of Biotechnology
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Chinese hamster ovary (CHO) cells are the predominant cell factory for the production of recombinant therapeutic proteins. Nevertheless, the lack in publicly available sequence information is severely limiting advances in CHO cell biology, including the exploration of microRNAs (miRNA) as tools for CHO cell characterization and engineering. In an effort to identify and annotate both conserved and novel CHO miRNAs in the absence of a Chinese hamster genome, we deep-sequenced small RNA fractions
doi:10.1016/j.jbiotec.2011.02.011
pmid:21392545
pmcid:PMC3119918
fatcat:lck5stsdrzc37gsmtom3k2ecnq
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... f 6 biotechnologically relevant cell lines and mapped the resulting reads to an artificial reference sequence consisting of all known miRNA hairpins. Read alignment patterns and read count ratios of 5 and 3 mature miRNAs were obtained and used for an independent classification into miR/miR* and 5p/3p miRNA pairs and discrimination of miRNAs from other non-coding RNAs, resulting in the annotation of 387 mature CHO miRNAs. The quantitative content of next-generation sequencing data was analyzed and confirmed using qPCR, to find that miRNAs are markers of cell status. Finally, cDNA sequencing of 26 validated targets of miR-17-92 suggests conserved functions for miRNAs in CHO cells, which together with the now publicly available sequence information sets the stage for developing novel RNAi tools for CHO cell engineering.
Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates
2016
Gene
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Braeken K, Moris M, Daniels R, Vanderleyden J, Michiels J (2006) New horizons for (p)ppGpp in bacterial and plant physiology. Trends Microbiol 14:45-54. ...
Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter FJ, Zakrzewski M, Goesmann A (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 10:154. ...
doi:10.1016/j.gene.2016.05.045
pmid:27259668
fatcat:hwivczylzfcgjom3ydqycjqtke
Specific surface glycan decorations enable antimicrobial peptide resistance in plant-beneficial pseudomonads with insect-pathogenic properties
2016
Environmental Microbiology
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., Doppmeier, D., Pühler, A., Vorhölter, F.J., Zakrzewski, M., and Goesmann, 550 A. (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. 551 BMC Bioinformatics 10: 154 ...
MBio 1: e00189-10. 586 Jousset, A., Schuldes, J., Keel, C., Maurhofer, M., Daniel, R., Scheu, S., and Thuermer, A. (2014) 587 Full-genome sequence of the plant growth-promoting bacterium Pseudomonas protegens ...
doi:10.1111/1462-2920.13571
pmid:27727519
fatcat:wpgm2z3u2ze67lsvcko3ev7cd4
Source Code des Corpus der Drucksachen des Deutschen Bundestages (CDRS-BT-Source)
[article]
2021
Zenodo
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0.0492472
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Dominke, Vera
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Donhauser, Anton
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Doppmeier ...
, Hans
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Daniels, Wolfgang
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Dannebom, Otto
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doi:10.5281/zenodo.4643068
fatcat:uffml53ykjfozgmny6xe45bcom