Integrative detection of genome-wide translation using iRibo
Summary: Ribosome profiling is a sequencing technique that provides a global picture of translation across a genome. Here, we present iRibo, a software program for integrating any number of ribosome profiling samples to obtain sensitive inference of annotated or unannotated translated open reading f...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723007931 |
| _version_ | 1827382466770370560 |
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| author | Alistair Turcan Jiwon Lee Aaron Wacholder Anne-Ruxandra Carvunis |
| author_facet | Alistair Turcan Jiwon Lee Aaron Wacholder Anne-Ruxandra Carvunis |
| author_sort | Alistair Turcan |
| collection | DOAJ |
| description | Summary: Ribosome profiling is a sequencing technique that provides a global picture of translation across a genome. Here, we present iRibo, a software program for integrating any number of ribosome profiling samples to obtain sensitive inference of annotated or unannotated translated open reading frames. We describe the process of using iRibo to generate a species’ translatome from a set of ribosome profiling samples using S. cerevisiae as an example.For complete details on the use and execution of this protocol, please refer to Wacholder et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-08T14:21:00Z |
| format | Article |
| id | doaj.art-4e73c37c392547a68ea04100fc3609ea |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-08T14:21:00Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-4e73c37c392547a68ea04100fc3609ea2024-01-14T05:40:06ZengElsevierSTAR Protocols2666-16672024-03-0151102826Integrative detection of genome-wide translation using iRiboAlistair Turcan0Jiwon Lee1Aaron Wacholder2Anne-Ruxandra Carvunis3Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Corresponding authorDepartment of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USADepartment of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Corresponding authorDepartment of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Corresponding authorSummary: Ribosome profiling is a sequencing technique that provides a global picture of translation across a genome. Here, we present iRibo, a software program for integrating any number of ribosome profiling samples to obtain sensitive inference of annotated or unannotated translated open reading frames. We describe the process of using iRibo to generate a species’ translatome from a set of ribosome profiling samples using S. cerevisiae as an example.For complete details on the use and execution of this protocol, please refer to Wacholder et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723007931BioinformaticsSequence analysisGenomicsModel Organisms |
| spellingShingle | Alistair Turcan Jiwon Lee Aaron Wacholder Anne-Ruxandra Carvunis Integrative detection of genome-wide translation using iRibo STAR Protocols Bioinformatics Sequence analysis Genomics Model Organisms |
| title | Integrative detection of genome-wide translation using iRibo |
| title_full | Integrative detection of genome-wide translation using iRibo |
| title_fullStr | Integrative detection of genome-wide translation using iRibo |
| title_full_unstemmed | Integrative detection of genome-wide translation using iRibo |
| title_short | Integrative detection of genome-wide translation using iRibo |
| title_sort | integrative detection of genome wide translation using iribo |
| topic | Bioinformatics Sequence analysis Genomics Model Organisms |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723007931 |
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