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Optimization of ribosomal RNA profile alignments

E. A. O'Brien, C. Notredame, D. G. Higgins
1998 Bioinformatics  
Acknowledgements The authors thank Richard Durbin for suggesting the use of the 1/d weights. We also thank Manolo Gouy for his help with rRNA sequences in general.  ...  Introduction Ribosomal RNA sequences (rRNA) are widely used to estimate the phylogenetic relatedness of groups of organisms (e.g.  ...  In this paper, we examine, empirically, the effectiveness of profile alignment methods for the alignment of RNA sequences.  ... 
doi:10.1093/bioinformatics/14.4.332 pmid:9632828 fatcat:xv7mj2s6jrb2zgrmpnde32qcwe

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2

Steven Busan, Kevin M. Weeks
2017 RNA: A publication of the RNA Society  
(B) Empirical evaluation of 5' side versus 3' side realignment of ambiguously located mutations using the E. coli ribosomal RNA dataset.  ...  Mutation profiles were evaluated against the E. coli ribosome structure from the Comparative RNA Web Site (Cannone et al. 2002) . Fig. 2 .  ... 
doi:10.1261/rna.061945.117 pmid:29114018 fatcat:7skkyrivfnfc3bcoqf2wzeslzm

Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX

Aikaterini Alexaki, Jacob Kames, Gaya K. Hettiarachchi, John C. Athey, Upendra K. Katneni, Ryan C. Hunt, Nobuko Hamasaki-Katagiri, David D. Holcomb, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
2020 F1000Research  
The ribosome profiling data are composed of Ribo-seq (mRNA sequencing data from ribosome protected fragments) and RNA-seq data (total RNA sequencing).  ...  Ribosome profiling provides the opportunity to evaluate translation kinetics at codon level resolution. Here, we describe ribosome profiling data, generated from two HEK293T cell lines.  ...  Ribosome profiling data typically consist of a set of sequences of ribosome protected fragments (RPF), designated as Ribo-seq data, which is accompanied by sequences from total RNA (RNA-seq).  ... 
doi:10.12688/f1000research.22400.1 pmid:33014344 pmcid:PMC7509596 fatcat:ruav275njjfffcz3lkolpyh524

GWIPS-viz: development of a ribo-seq genome browser

Audrey M. Michel, Gearoid Fox, Anmol M. Kiran, Christof De Bo, Patrick B. F. O'Connor, Stephen M. Heaphy, James P. A. Mullan, Claire A. Donohue, Desmond G. Higgins, Pavel V. Baranov
2013 Nucleic Acids Research  
It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified.  ...  We describe the development of GWIPS-viz (http:// gwips.ucc.ie), an online genome browser for viewing ribosome profiling data.  ...  To date, there have been two main strategies of ribosome profiling: ribosome profiling of initiating ribosomes and ribosome profiling of elongating ribosomes.  ... 
doi:10.1093/nar/gkt1035 pmid:24185699 pmcid:PMC3965066 fatcat:otryfevmjje3ddubxfnlquwalq

Nuclease-mediated depletion biases in ribosome footprint profiling libraries [article]

Boris Zinshteyn, Jamie R Wangen, Boyang Hua, Rachel Green
2020 bioRxiv   pre-print
Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them unsuitable for ribosome footprint profiling.  ...  the ends of RNA fragments.  ...  same method can be adapted to ribosome profiling, which has a much more biased distribution of rRNA fragments than RNA-seq.  ... 
doi:10.1101/2020.03.30.017061 fatcat:kq7izjfrn5ck7kbh3atm26ouzq

Translation elongation and mRNA stability are coupled through the ribosomal A-site

Gavin Hanson, Najwa Alhusaini, Nathan Morris, Thomas Sweet, Jeff Coller
2018 RNA: A publication of the RNA Society  
The ribosome profiling reads were then aligned against an index of S. cerevisiae ribosomal RNA sequences from Ensembl using bowtie with the following parameters: -D 15 -R 2-N 1 -L 25 -I S,1,0.75.  ...  Sequences that failed to align to the ribosomal RNA index were taken to be from messenger RNA and were aligned to the entire S. cerevisiae genome using HISAT2, with release 84 of Ensembl's gene annotations  ...  is the average elongation rate based on the actual codon sequence of the transcript.  ... 
doi:10.1261/rna.066787.118 pmid:29997263 fatcat:a647ww56djgaro24hc7oau24xa

The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria

Gene-Wei Li, Eugene Oh, Jonathan S. Weissman
2012 Nature  
This spacing coincides with the optimal spacing for ribosome binding at start codons 21 .  ...  Here we present a genomewide analysis of translational pausing in bacteria by ribosome profiling-deep sequencing of ribosome-protected mRNA fragments 3-5 .  ...  Elf and members of the Weissman laboratory for discussions; J. Dunn for ribosome profiling data on S. cerevisiae; C. Chu for help with sequencing; and J.  ... 
doi:10.1038/nature10965 pmid:22456704 pmcid:PMC3338875 fatcat:amiajnvdhzhclo4uuv5zti77vi

Ribo-Zero Gold Kit: improved RNA-seq results after removal of cytoplasmic and mitochondrial ribosomal RNA

Vladimir Benes, Jonathon Blake, Ken Doyle
2011 Nature Methods  
Ribo-Zero Gold Kit: improved RNA-seq results after removal of cytoplasmic and mitochondrial ribosomal RNA Ribosomal RNA (rRNA) constitutes the majority (>98%) of total RNA preparations.  ...  Here, we describe the Ribo-Zero Gold Kit: an improvement to the original Ribo-Zero method that allows removal of mitochondrial as well as cytoplasmic rRNA from total RNA preparations.  ...  Figure 2 | 2 (a,b) Profiles of RNA-seq libraries prepared after treatment with the Ribo-Zero (a) and Ribo-Zero Gold (b) Kits. Figure 1 | 1 Removal of ribosomal RNAs from total RNA.  ... 
doi:10.1038/nmeth.f.352 fatcat:pdnmvew6abhuxl7ienllx36kk4

Transcriptome-wide measurement of translation by ribosome profiling

Nicholas J. McGlincy, Nicholas T. Ingolia
2017 Methods  
The ribosome profiling method provides us with an opportunity to learn these locations, by sequencing a cDNA library derived from the short fragments of mRNA covered by the ribosome.  ...  Since its original description, the ribosome profiling method has undergone continuing development; in this article we describe the method's current state.  ...  Acknowledgments We would like to thank all the members of the Ingolia and Lareau labs for providing a constructive and exciting environment within which to study ribosome profiling.  ... 
doi:10.1016/j.ymeth.2017.05.028 pmid:28579404 pmcid:PMC5582988 fatcat:ngjpove2d5dsdodkfuy6tz25pu

Super-resolution ribosome profiling reveals unannotated translation events inArabidopsis

Polly Yingshan Hsu, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li, Carl J. Rothfels, Uwe Ohler, Philip N. Benfey
2016 Proceedings of the National Academy of Sciences of the United States of America  
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation.  ...  Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms. translation | ribosome footprint | Ribo-seq | ncRNA | sORF  ...  S1 Optimization of ribosome profiling in Arabidopsis.  ... 
doi:10.1073/pnas.1614788113 pmid:27791167 pmcid:PMC5111709 fatcat:zkijbn2hvramdota7rz4hozf4m

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data

Jordan A. Berg, Jonathan R. Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter, Aaron E. Darling
2020 PLoS Computational Biology  
ribosome profiling.  ...  Ribosome profiling, an application of nucleic acid sequencing for monitoring ribosome activity, has revolutionized our understanding of protein translation dynamics.  ...  Howard for helpful discussions concerning ribosome profiling and sequencing analysis. The authors also wish to thank Mark E. Wadsworth, Ryan Miller, and Michael J.  ... 
doi:10.1371/journal.pcbi.1007625 pmid:32004313 pmcid:PMC7015430 fatcat:flsraa7x6zazthb2tl2wmrrfh4

Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion

Thomas Beuchert Kallehauge, Shangzhong Li, Lasse Ebdrup Pedersen, Tae Kwang Ha, Daniel Ley, Mikael Rørdam Andersen, Helene Faustrup Kildegaard, Gyun Min Lee, Nathan E. Lewis
2017 Scientific Reports  
Acknowledgements The authors would like to thank Sara Petersen Bjørn for the assistance of cloning and sequencing of the heavyand light chain genes.  ...  SL was supported with funding from the Frontiers of Innovation Scholars Program at UCSD.  ...  (A) Schematic representation of ribosome profiling workflow in which Ribo-Seq and RNA-Seq data were simultaneously generated.  ... 
doi:10.1038/srep40388 pmid:28091612 pmcid:PMC5238448 fatcat:lr42wc6hp5dttjfrlliwklzoue

RP-REP Ribosomal Profiling Reports: an open-source cloud-enabled framework for reproducible ribosomal profiling data processing, analysis, and result reporting

Travis L. Jensen, William F. Hooper, Sami R. Cherikh, Johannes B. Goll
2021 F1000Research  
RP-REP automatically executes a series of customizable steps including filtering of contaminant RNA, enrichment of true ribosomal footprints, reference alignment and gene translation quantification, gene  ...  Here we present Ribosomal Profiling Reports (RP-REP), a new open-source cloud-enabled software that allows users to execute start-to-end gene-level ribosomal profiling and RNA-Seq analysis on a pre-configured  ...  During processing of ribosomal profiling data, reads that fall outside the typical length range of ribosomal footprints (25 nt to 35 nt) are removed.  ... 
doi:10.12688/f1000research.40668.1 fatcat:glmalivcxrc6fpb2g7u3p6ykjy

The extent of ribosome queuing in budding yeast

Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava, Tamir Tuller, John McCarthy
2018 PLoS Computational Biology  
Here we present an experimental-computational approach for studying ribosome queuing based on sequencing of RNA footprints extracted from pairs of ribosomes (dRPFs) using a modified ribosome profiling  ...  We combine our approach with traditional ribosome profiling to generate a detailed profile of ribosome traffic. The data are analyzed using computational models of translation dynamics.  ...  A.D. is grateful to the Azrieli Foundation for the award of an Azrieli Fellowship. This study was supported in part by a fellowship from the Edmond J.  ... 
doi:10.1371/journal.pcbi.1005951 pmid:29377894 pmcid:PMC5805374 fatcat:auedfpg6ozfghgqc4fsjbaxxom

riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data [article]

Fabio Lauria, Toma Tebaldi, Paola Bernabo, Ewout J. N. Groen, Thomas H. Gillingwater, Gabriella Viero
2017 bioRxiv   pre-print
Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs.  ...  Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine trinucleotide periodicity of translating ribosomes  ...  (C) An example of ribosome occupancy profile obtained from the alignment of the 5' and the 3' end of reads around the start codon (reads length, 28 nucleotides) is superimposed to the schematic representation  ... 
doi:10.1101/169862 fatcat:fqv6gwafybbkzc5ws5rx4pm5e4
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