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RiboA: a web application to identify ribosome A-site locations in ribosome profiling data
BACKGROUND: Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identif...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7992832/ https://www.ncbi.nlm.nih.gov/pubmed/33765913 http://dx.doi.org/10.1186/s12859-021-04068-w |
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author | Shao, Danying Ahmed, Nabeel Soni, Nishant O’Brien, Edward P. |
author_facet | Shao, Danying Ahmed, Nabeel Soni, Nishant O’Brien, Edward P. |
author_sort | Shao, Danying |
collection | PubMed |
description | BACKGROUND: Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. RESULTS: We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. CONCLUSIONS: The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license. |
format | Online Article Text |
id | pubmed-7992832 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-79928322021-03-25 RiboA: a web application to identify ribosome A-site locations in ribosome profiling data Shao, Danying Ahmed, Nabeel Soni, Nishant O’Brien, Edward P. BMC Bioinformatics Software BACKGROUND: Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. RESULTS: We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. CONCLUSIONS: The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license. BioMed Central 2021-03-25 /pmc/articles/PMC7992832/ /pubmed/33765913 http://dx.doi.org/10.1186/s12859-021-04068-w Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Shao, Danying Ahmed, Nabeel Soni, Nishant O’Brien, Edward P. RiboA: a web application to identify ribosome A-site locations in ribosome profiling data |
title | RiboA: a web application to identify ribosome A-site locations in ribosome profiling data |
title_full | RiboA: a web application to identify ribosome A-site locations in ribosome profiling data |
title_fullStr | RiboA: a web application to identify ribosome A-site locations in ribosome profiling data |
title_full_unstemmed | RiboA: a web application to identify ribosome A-site locations in ribosome profiling data |
title_short | RiboA: a web application to identify ribosome A-site locations in ribosome profiling data |
title_sort | riboa: a web application to identify ribosome a-site locations in ribosome profiling data |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7992832/ https://www.ncbi.nlm.nih.gov/pubmed/33765913 http://dx.doi.org/10.1186/s12859-021-04068-w |
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