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TBro: visualization and management of de novo transcriptomes
RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absenc...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199188/ https://www.ncbi.nlm.nih.gov/pubmed/28025338 http://dx.doi.org/10.1093/database/baw146 |
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author | Ankenbrand, Markus J. Weber, Lorenz Becker, Dirk Förster, Frank Bemm, Felix |
author_facet | Ankenbrand, Markus J. Weber, Lorenz Becker, Dirk Förster, Frank Bemm, Felix |
author_sort | Ankenbrand, Markus J. |
collection | PubMed |
description | RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro’s modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers. Database URL: tbro.carnivorom.com |
format | Online Article Text |
id | pubmed-5199188 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-51991882017-01-06 TBro: visualization and management of de novo transcriptomes Ankenbrand, Markus J. Weber, Lorenz Becker, Dirk Förster, Frank Bemm, Felix Database (Oxford) Original Article RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro’s modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers. Database URL: tbro.carnivorom.com Oxford University Press 2016-12-26 /pmc/articles/PMC5199188/ /pubmed/28025338 http://dx.doi.org/10.1093/database/baw146 Text en © The Author(s) 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Ankenbrand, Markus J. Weber, Lorenz Becker, Dirk Förster, Frank Bemm, Felix TBro: visualization and management of de novo transcriptomes |
title | TBro: visualization and management of de novo transcriptomes |
title_full | TBro: visualization and management of de novo transcriptomes |
title_fullStr | TBro: visualization and management of de novo transcriptomes |
title_full_unstemmed | TBro: visualization and management of de novo transcriptomes |
title_short | TBro: visualization and management of de novo transcriptomes |
title_sort | tbro: visualization and management of de novo transcriptomes |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199188/ https://www.ncbi.nlm.nih.gov/pubmed/28025338 http://dx.doi.org/10.1093/database/baw146 |
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