TSSAR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TSSAR
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Tool usage distribution map

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TSSAR specifications

Information


Unique identifier OMICS_03523
Name TSSAR
Interface Web user interface
Restrictions to use None
Programming languages Java, Perl, R
License Apache License version 2.0, GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Download


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Maintainer


  • person_outline Fabian Amman

Additional information


http://nibiru.tbi.univie.ac.at/TSSAR/workflow

Publication for TSSAR

TSSAR citations

 (7)
library_books

Nitrogen cost minimization is promoted by structural changes in the transcriptome of N deprived Prochlorococcus cells

2017
PMCID: 5607370
PMID: 28585937
DOI: 10.1038/ismej.2017.88

[…] cription is defined as a verified saw-tooth pattern of transcript reads mapping downstream of a gene’s annotated start site. Verification of the saw-tooth pattern was performed manually after running TSSAR. The internal transcription ratio is defined as the ratio of read abundance at the internal TSS compared to the abundance of reads at the primary TSS. The internal transcription ratio generally […]

library_books

Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily

2016
Sci Rep
PMCID: 5015018
PMID: 27605472
DOI: 10.1038/srep31597

[…] turer’s instructions to remove residual DNA contamination.RNA-seq was carried out by vertis Biotechnologie. Data analysis was carried out using the Tuxedo protocol for analysis of gene expression and TSSAR webservice for dRNA transcription start site analysis. In addition a manual visual processing approach was carried out for each. […]

library_books

ReadXplorer 2—detailed read mapping analysis and visualization from one single source

2016
Bioinformatics
PMCID: 5167064
PMID: 27540267
DOI: 10.1093/bioinformatics/btw541

[…] actice to exclude reads mapping to more than a single position from downstream analyses () and many read mapping analysis tools do not address multiple mapped reads (e.g. TSSPredator (), TSSer () and TSSAR () for TSS detection or VarScan 2 [() for single nucleotide polymorphism (SNP) detection]. For the latter tools, we assume that they incorporate all reads present in the data set provided by the […]

library_books

Genome wide transcription start site profiling in biofilm grown Burkholderia cenocepacia J2315

2015
BMC Genomics
PMCID: 4603805
PMID: 26462475
DOI: 10.1186/s12864-015-1993-3

[…] Mapping output from dRNA-Seq was split by replicon and coverted to SAM format (using samtools 1.2). Those SAM files were used as input for TSSAR, a tool for automated de novo TSS annotation [], to map all loci with coverage maxima which are enriched in the TEX-treated library. Default parameters (p-value threshold 0.001, noise threshold […]

library_books

Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs

2015
PLoS Genet
PMCID: 4376681
PMID: 25816203
DOI: 10.1371/journal.pgen.1005087

[…] sed to detect genomic positions, where the difference of observed read starts significantly exceeds the difference of expected read starts. These positions are then defined as TSS. We further applied TSSAR [], an implementation of the dRNA-seq TSS detection method, on our RNA-seq data. Different to the standard dRNA-seq experimental setup, the background distribution of read starts was obtained fr […]

library_books

The primary transcriptome of the marine diazotroph Trichodesmium erythraeum IMS101

2014
Sci Rep
PMCID: 4143802
PMID: 25155278
DOI: 10.1038/srep06187

[…] ative (samples of just discarded or just predicted TSS were verified manually) possibly producing false-negative TSS.To test for statistical significance, the 6,080 predicted TSS were compared with a TSSAR TSS annotation. For 5,542 (91.15%) of our predicted TSS, a TSS (p < 0.05, noise threshold = 10) was also annotated by TSSAR within ±10 nt. Furthermore, 249 of the 538 unconfirmed TSS are located […]


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TSSAR institution(s)
Bioinformatics Group, Department of Computer Science and the Interdisciplinary Center for Bioinformatic, University of Leipzig, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria; Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria; Center for RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Santa Fe Institute, Santa Fe, NM, USA; Research group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
TSSAR funding source(s)
Supported by the Austrian Science Fund (FWF) projects “In silico annotation of noncoding RNAs and their targets” (AF 0430511), “RNA regulation of the transcriptome” (F43), the German ministry of science (0316165C as part of the e:Bio initiative), and the Deutsche Forschungsgemeinschaft (STA 850/10–2 within the SPP 1258 “Sensory and regulatory RNAs in Prokaryotes”).

TSSAR review

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Amr Galal

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Web
The tools is great, powerful and better than others for detect TSS
just the web tool doesn't give same results as the stand alone one using same parameters