Janus--a comprehensive tool investigating the two faces of transcription
| Autor: | Daniela Esser, Jan W. P. Kuiper, Matthias Barann, Tuuli Lappalainen, Anne Luzius, Philip Rosenstiel, Inga Vater, Ulrich C. Klostermeier, Vyacheslav Amstislavskiy, Ralf Sudbrak, Reiner Siebert, Stefan Schreiber, Ole Ammerpohl, Hans Lehrach |
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| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Statistics and Probability
Computational biology Biology Biochemistry Genome World Wide Web 03 medical and health sciences 0302 clinical medicine Software Transcription (biology) Humans RNA Antisense Janus Molecular Biology 030304 developmental biology Cell Line Transformed Supplementary data 0303 health sciences business.industry Gene Expression Profiling Genetic Variation High-Throughput Nucleotide Sequencing DNA Methylation Computer Science Applications Gene expression profiling Computational Mathematics Antisense Orientation Computational Theory and Mathematics 030220 oncology & carcinogenesis DNA methylation business |
| Zdroj: | Bioinformatics; Vol 29 Bioinformatics |
| ISSN: | 1367-4803 |
| DOI: | 10.1093/bioinformatics/btt185 |
| Popis: | Motivation: Protocols to generate strand-specific transcriptomes with next-generation sequencing platforms have been used by the scientific community roughly since 2008. Strand-specific reads allow for detection of antisense events and a higher resolution of expression profiles enabling extension of current transcript annotations. However, applications making use of this strandedness information are still scarce. Results: Here we present a tool (Janus), which focuses on the identification of transcriptional active regions in antisense orientation to known and novel transcribed elements of the genome. Janus can compare the antisense events of multiple samples and assigns scores to identify mutual expression of either transcript in a sense/ antisense pair, which could hint to regulatory mechanisms. Janus is able to make use of single-nucleotide variant (SNV) and methylation data, if available, and reports the sense to antisense ratio of regions in the vicinity of the identified genetic and epigenetic variation. Janus interrogates positions of heterozygous SNVs to identify strand-specific allelic imbalance. Availability: Janus is written in C/Cþþ and freely available at http:// www.ikmb.uni-kiel.de/janus/janus.html under terms of GNU General Public License, for both, Linux and Windows 64� . Although the binaries will work without additional downloads, the software depends on bamtools (https://github.com/pezmaster31/bamtools) for compilation. A detailed tutorial section is included in the first section of the supplemental material and included as brief readme.txt in the tutorial archive. Contact: m.barann@mucosa.de or p.rosenstiel@mucosa.de Supplementary information: Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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