ReadXplorer - Visualization and Analysis of Mapped Sequences

Hilker, Rolf; Stadermann, Kai Bernd; Doppmeier, Daniel; Kalinowski, Jörn; Stoye, Jens; Straube, Jasmin; Winnebald, Jörn; Goesmann, Alexander

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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DOI

https://doi.org/10.1093/bioinformatics/btu205

Autor*in

Hilker, Rolf^UniBi; Stadermann, Kai Bernd^UniBi ; Doppmeier, Daniel^UniBi; Kalinowski, Jörn^UniBi; Stoye, Jens^UniBi ; Straube, Jasmin^UniBi; Winnebald, Jörn^UniBi; Goesmann, Alexander

Einrichtung

Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie

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

Ausgabe

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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Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A.
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Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase.
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Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment.
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Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape.
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