ArticlePloS one2014
TraV: a genome context sensitive transcriptome browser.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- Antisense transcription is associated with expression of metal resistance determinants in Cupriavidus metallidurans CH34.Metallomics : integrated biometal science · 2024Article
- Novel insights into phage biology of the pathogenFrontiers in microbiology · 2024Article
- Modulation ofFrontiers in genetics · 2022Article
- Closely RelatedViruses · 2020Article
- Interplay between the Zur Regulon Components and Metal Resistance in Cupriavidus metallidurans.Journal of bacteriology · 2019Article
- BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes.Frontiers in microbiology · 2018Article
- Small RNA mediated repression of subtilisin production in Bacillus licheniformis.Scientific reports · 2017Article
- FnrL and Three Dnr Regulators Are Used for the Metabolic Adaptation to Low Oxygen Tension inFrontiers in microbiology · 2017Article
- A survey of best practices for RNA-seq data analysis.Genome biology · 2016Review
- TBro: visualization and management of de novo transcriptomes.Database : the journal of biological databases and curation · 2016Article
- A Terpene Synthase Is Involved in the Synthesis of the Volatile Organic Compound Sodorifen of Serratia plymuthica 4Rx13.Frontiers in microbiology · 2016Article
- Genome-based identification of active prophage regions by next generation sequencing in Bacillus licheniformis DSM13.PloS one · 2015Article
- Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.GigaScience · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) technologies like Illumina and ABI Solid enable the investigation of transcriptional activities of genomes. While read mapping tools have been continually improved to enable the processing of the increasing number of reads generated by NGS technologies, analysis and visualization tools are struggling with the amount of data they are presented with. Current tools are capable of handling at most two to three datasets simultaneously before they are limited by available memory or due to processing overhead. In order to process fifteen transcriptome sequencing experiments of Bacillus licheniformis DSM13 obtained in a previous study, we developed TraV, a RNA-Seq analysis and visualization tool. The analytical methods are designed for prokaryotic RNA-seq experiments. TraV calculates single nucleotide activities from the mapping information to visualize and analyze multiple transcriptome sequencing experiments. The use of nucleotide activities instead of single read mapping information is highly memory efficient without incurring a processing overhead. TraV is available at http://appmibio.uni-goettingen.de/index.php?sec=serv.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.