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ReadXplorer—visualization and analysis of mapped sequences

Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann
2014 Bioinformatics  
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
more » ... 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.
doi:10.1093/bioinformatics/btu205 pmid:24790157 pmcid:PMC4217279 fatcat:i6o7gvzc7zbmvn4cg3nbnwlvke

EDGAR: A software framework for the comparative analysis of prokaryotic genomes

Jochen Blom, Stefan P Albaum, Daniel Doppmeier, Alfred Puhler, Frank-Jorg Vorholter, Martha Zakrzewski, Alexander Goesmann
2009 BMC Bioinformatics  
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
more » ... 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.
doi:10.1186/1471-2105-10-154 pmid:19457249 pmcid:PMC2696450 fatcat:wk2r5gvhufginazad346jk4vxu

Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering

Matthias Hackl, Tobias Jakobi, Jochen Blom, Daniel Doppmeier, Karina Brinkrolf, Rafael Szczepanowski, Stephan H. Bernhart, Christian Höner zu Siederdissen, Juan A. Hernandez Bort, Matthias Wieser, Renate Kunert, Simon Jeffs (+5 others)
2011 Journal of Biotechnology  
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
more » ... 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.
doi:10.1016/j.jbiotec.2011.02.011 pmid:21392545 pmcid:PMC3119918 fatcat:lck5stsdrzc37gsmtom3k2ecnq

Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates

Liberata Mwita, Wai Yin Chan, Theresa Pretorius, Sylvester L. Lyantagaye, Svitlana V. Lapa, Lilia V. Avdeeva, Oleg N. Reva
2016 Gene  
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

Peter Kupferschmied, Tiancong Chai, Pascale Flury, Jochen Blom, Theo H.M. Smits, Monika Maurhofer, Christoph Keel
2016 Environmental Microbiology  
., 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]

Sean Fobbe
2021 Zenodo  
0.0492472 0.05 14.48 Dominke, Vera 96 0.0141549 0.01 14.50 Donhauser, Anton 64 0.0094366 0.01 14.50 Donth, Michael 6 0.0008847 0.00 14.51 Dopatka, Wilhelm 5 0.0007372 0.00 14.51 Doppmeier  ...  , Hans 20 0.0029489 0.00 13.21 Daniels, Wolfgang 112 0.0165140 0.02 13.22 Dann, Heidemarie 30 0.0044234 0.00 13.23 Dannebom, Otto 19 0.0028015 0.00 13.23 Dannemann, Robert 92  ... 
doi:10.5281/zenodo.4643068 fatcat:uffml53ykjfozgmny6xe45bcom