TSSer specifications

Information


Unique identifier OMICS_02191
Name TSSer
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained No

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Publication for TSSer

TSSer in publications

 (7)
PMCID: 5687710
PMID: 29141011
DOI: 10.1371/journal.pone.0187243

[…] decade, several improvements in the promoter prediction process were made. troukhan [] combined positional frequency of 5′ est matches onto genomic dna with the gene models. this approach, known as tsser, is, in a nutshell, a deterministic method that predicts one transcription start site per locus. for arabidopsis thaliana promoters, it achieves remarkable accuracy. however, even […]

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

[…] common practice 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 […]

PMCID: 4991838
PMID: 27436340
DOI: 10.1093/dnares/dsw029

[…] near the tss of active genes would be lower than at silent genes. based on read density at known tsss and dhss from the encode project and using de novo methods of tss prediction (e.g. npest or tsser), it is possible to sort tsss according to transcriptional activity of corresponding genes. in the near future, it may be feasible to quantitatively reconstruct gene expression patterns […]

PMCID: 4829306
PMID: 26950529
DOI: 10.1080/15476286.2016.1146855

[…] experiment was combined with that of the tex-treated rna-seq sample. this method, also referred to as differential rna-seq (drna-seq), was applied in combination with the tss prediction program tsser. tsser predicted 1819 tsss, of which 884 are primary, 744 are orphan, 66 are internal and 125 are antisense (table s9). a significantly higher number of orphan tsss and antisense tsss […]

PMCID: 4494643
PMID: 26001787
DOI: 10.1186/s12862-015-0368-3

[…] 500 bootstrap replicates. analyses were conducted in in mega5 []. ediv = eurolophosaurus divaricatus (og); this = t. hispidus (og); ttor = t. torquatus (og); tpin = t. pinima; thel = t. helenae; tsser = t. semitaeniatus from seridó, rio grande do norte state; tss = t. semitaeniatus south of the sfr; tsne = t. semitaeniatus northeast of the sfr; tsnw = t. semitaeniatus northwest of the sfr; […]


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TSSer institution(s)
Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
TSSer funding source(s)
Supported by the University of Basel and the Swiss National Science Foundation (grant number 31003A_147013).

TSSer review

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Amr Galal

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Desktop
TSSer was a revolution in TSS automate detection and used very good statistical hypothesis but existing of new tools more powerful could give better results