PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data
| dc.contributor.author | Kumari, Romika | |
| dc.contributor.author | Michel, Audrey M. | |
| dc.contributor.author | Baranov, Pavel V. | |
| dc.contributor.funder | Science Foundation Ireland | en |
| dc.date.accessioned | 2022-03-04T16:18:29Z | |
| dc.date.available | 2022-03-04T16:18:29Z | |
| dc.date.issued | 2018-07-26 | |
| dc.date.updated | 2022-03-04T16:12:02Z | |
| dc.description.abstract | The process of translation is characterized by irregularities in the local decoding rates of specific mRNA codons. This includes the occurrences of long pauses that can take place when ribosomes decode certain peptide sequences, encounter strong RNA secondary structures, or decode "hungry" codons. Examples are known where such pausing or stalling is used for regulating protein synthesis. This can be achieved at the level of translation via direct alteration of ribosome progression through mRNA or by altering mRNA stability via NoGo decay. Ribosome pausing has also been implicated in the cotranslational folding of proteins. Ribosome profiling data often are used for inferring the locations of ribosome pauses. However, no dedicated online software is available for this purpose. Here we present PausePred (https://pausepred. ucc. ie/), which can be used to infer ribosome pauses from ribosome profiling (Ribo-seq) data. Peaks of ribosome footprint density are scored based on their magnitude relative to the background density within the surrounding area. The scoring allows the comparison of peaks across the transcriptome or genome. In addition to the score, PausePred reports the coordinates of the pause, the footprint density at the pause site, and the surrounding nucleotide sequence. The pauses can be visualized in the context of Ribo-seq and RNA-seq density plots generated for specific transcripts or genomic regions with the Rfeet tool. PausePred does not require input on the location of protein coding ORFs (although gene annotations can be optionally supplied). As a result, it can be used universally and its output does not depend on ever evolving annotations. | en |
| dc.description.status | Peer reviewed | en |
| dc.description.version | Published Version | en |
| dc.format.mimetype | application/pdf | en |
| dc.identifier.citation | Kumari, R., Michel, A. M. and Baranov, P. V. (2018) 'PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data'', Rna-A Publication of The Rna Society, 24, pp. 1297-1304. doi:10.1261/rna.065235.117 | en |
| dc.identifier.doi | 10.1261/rna.065235.117 | en |
| dc.identifier.endpage | 1304 | en |
| dc.identifier.issn | 1355-8382 | |
| dc.identifier.journaltitle | RNA - A Publication of The RNA Society | en |
| dc.identifier.startpage | 1297 | en |
| dc.identifier.uri | https://hdl.handle.net/10468/12749 | |
| dc.identifier.volume | 24 | en |
| dc.language.iso | en | en |
| dc.publisher | Cold Spring Harbor Laboratory Press | en |
| dc.relation.project | info:eu-repo/grantAgreement/SFI/SFI Investigator Programme/12/IA/1335/IE/Development of computational resources for the analysis of Genome Wide Information on Protein Synthesis (GWIPS)./ | en |
| dc.relation.uri | https://rnajournal.cshlp.org/content/24/10/1297.short | |
| dc.rights | © 2018 Kumari et al. This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. | en |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc/4.0/ | en |
| dc.subject | Ribosome pause | en |
| dc.subject | Translation | en |
| dc.subject | Ribo-seq | en |
| dc.subject | Ribosome profiling | en |
| dc.subject | Ribosome stalling | en |
| dc.title | PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data | en |
| dc.type | Article (peer-reviewed) | en |
