ReadXplorer - Visualization and Analysis of Mapped Sequences
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A (2014)
Bioinformatics 30(16): 2247-2254.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Einrichtung
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Centrum für Biotechnologie > Institut für Bioinformatik
Abstract / Bemerkung
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 and 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 open-source software at http://www.readxplorer.org along with a detailed manual.
CONTACT: rhilker@mikrobio.med.uni-giessen.de
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
The Author 2014. Published by Oxford University Press.
Erscheinungsjahr
2014
Zeitschriftentitel
Bioinformatics
Band
30
Ausgabe
16
Seite(n)
2247-2254
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/2674387
Zitieren
Hilker R, Stadermann KB, Doppmeier D, et al. ReadXplorer - Visualization and Analysis of Mapped Sequences. Bioinformatics. 2014;30(16):2247-2254.
Hilker, R., Stadermann, K. B., Doppmeier, D., Kalinowski, J., Stoye, J., Straube, J., Winnebald, J., et al. (2014). ReadXplorer - Visualization and Analysis of Mapped Sequences. Bioinformatics, 30(16), 2247-2254. doi:10.1093/bioinformatics/btu205
Hilker, Rolf, Stadermann, Kai Bernd, Doppmeier, Daniel, Kalinowski, Jörn, Stoye, Jens, Straube, Jasmin, Winnebald, Jörn, and Goesmann, Alexander. 2014. “ReadXplorer - Visualization and Analysis of Mapped Sequences”. Bioinformatics 30 (16): 2247-2254.
Hilker, R., Stadermann, K. B., Doppmeier, D., Kalinowski, J., Stoye, J., Straube, J., Winnebald, J., and Goesmann, A. (2014). ReadXplorer - Visualization and Analysis of Mapped Sequences. Bioinformatics 30, 2247-2254.
Hilker, R., et al., 2014. ReadXplorer - Visualization and Analysis of Mapped Sequences. Bioinformatics, 30(16), p 2247-2254.
R. Hilker, et al., “ReadXplorer - Visualization and Analysis of Mapped Sequences”, Bioinformatics, vol. 30, 2014, pp. 2247-2254.
Hilker, R., Stadermann, K.B., Doppmeier, D., Kalinowski, J., Stoye, J., Straube, J., Winnebald, J., Goesmann, A.: ReadXplorer - Visualization and Analysis of Mapped Sequences. Bioinformatics. 30, 2247-2254 (2014).
Hilker, Rolf, Stadermann, Kai Bernd, Doppmeier, Daniel, Kalinowski, Jörn, Stoye, Jens, Straube, Jasmin, Winnebald, Jörn, and Goesmann, Alexander. “ReadXplorer - Visualization and Analysis of Mapped Sequences”. Bioinformatics 30.16 (2014): 2247-2254.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
48 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
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Redox-Sensing Under Hypochlorite Stress and Infection Conditions by the Rrf2-Family Repressor HypR in Staphylococcus aureus.
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The guanidinobutyrase GbuA is essential for the alkylquinolone-regulated pyocyanin production during parasitic growth of Pseudomonas aeruginosa in co-culture with Aeromonas hydrophila.
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Jagmann N, Bleicher V, Busche T, Kalinowski J, Philipp B., Environ Microbiol 18(10), 2016
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Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq).
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ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
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Deciphering the Transcriptional Response Mediated by the Redox-Sensing System HbpS-SenS-SenR from Streptomycetes.
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Genome-Based Genetic Tool Development for Bacillus methanolicus: Theta- and Rolling Circle-Replicating Plasmids for Inducible Gene Expression and Application to Methanol-Based Cadaverine Production.
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An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH.
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A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L-fucose versus D-glucose.
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Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment.
Hilker R, Munder A, Klockgether J, Losada PM, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Fischer S, Peng H, Schönfelder T, Türk O, Wiehlmann L, Wölbeling F, Gulbins E, Goesmann A, Tümmler B., Environ Microbiol 17(1), 2015
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Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-myrcene biotransformation.
Soares-Castro P, Santos PM., Genome Biol Evol 7(1), 2015
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Soares-Castro P, Santos PM., Genome Biol Evol 7(1), 2015
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Transcriptional regulation of the vanillate utilization genes (vanABK Operon) of Corynebacterium glutamicum by VanR, a PadR-like repressor.
Morabbi Heravi K, Lange J, Watzlawick H, Kalinowski J, Altenbuchner J., J Bacteriol 197(5), 2015
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Morabbi Heravi K, Lange J, Watzlawick H, Kalinowski J, Altenbuchner J., J Bacteriol 197(5), 2015
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Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape.
Irla M, Neshat A, Brautaset T, Rückert C, Kalinowski J, Wendisch VF., BMC Genomics 16(), 2015
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Irla M, Neshat A, Brautaset T, Rückert C, Kalinowski J, Wendisch VF., BMC Genomics 16(), 2015
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Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome.
Nolla-Ardèvol V, Strous M, Tegetmeyer HE., Front Microbiol 6(), 2015
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