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Web application for automatic prediction of gene translation elongation efficiency

Vladimir Sokolov, Bulat Zuraev, Sergei Lashin, Yury Matushkin
2015 Journal of Integrative Bioinformatics  
In this study, a special EloE (Elongation Efficiency) web application is described.  ...  The EloE can be useful in preliminary estimation of translation elongation efficiency for genes for which experimental data are not available yet.  ...  Acknowledgments The work was partially supported by the Russian Foundation for Basic research (grant no. 13-04-00620) and budget project no. VI.61.1.2.  ... 
doi:10.2390/biecoll-jib-2015-256 pmid:26527190 fatcat:qojmjx3stjguncp55jiqp3e4ae

A web application for automatic prediction of gene translation elongation efficiency

Vladimir S. Sokolov, Bulat S. Zuraev, Sergei A. Lashin, Yury G. Matushkin
2015 Journal of Integrative Bioinformatics  
The EloE can be useful in preliminary estimation of translation elongation efficiency for genes for which experimental data are not available yet.  ...  In this study, a special EloE (Elongation Efficiency) web application is described.  ...  Acknowledgments The work was partially supported by the Russian Foundation for Basic research (grant no. 13-04-00620) and budget project no. VI.61.1.2.  ... 
doi:10.1515/jib-2015-256 fatcat:opn6q52muzh2vf7azz4nrhbql4

Computational resources for ribosome profiling: from database to Web server and software

Hongwei Wang, Yan Wang, Zhi Xie
2017 Briefings in Bioinformatics  
The increasing application of ribosome profiling in recent years has achieved remarkable progress toward understanding the composition, regulation and mechanism of translation.  ...  Ribosome profiling is emerging as a powerful technique that enables genome-wide investigation of in vivo translation at sub-codon resolution.  ...  In contrast, riboviz (www.riboviz.org) is a Web application for the convenient exploration and analysis of ribo-seq data.  ... 
doi:10.1093/bib/bbx093 pmid:28968766 fatcat:uq5zk3rkhvhvlkrbtfjevc5uim

ORFik: a comprehensive R toolkit for the analysis of translation

Håkon Tjeldnes, Kornel Labun, Yamila Torres Cleuren, Katarzyna Chyżyńska, Michał Świrski, Eivind Valen
2021 BMC Bioinformatics  
Background With the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics, there is a need for back-end functions and streamlined  ...  ORFik streamlines the steps to process, analyze, and visualize the different steps of translation with a particular focus on initiation and elongation.  ...  Acknowledgements We would like to thank the Bioconductor core team and community for providing valuable feedback for developing ORFik.  ... 
doi:10.1186/s12859-021-04254-w pmid:34147079 fatcat:dnzwtr5lijepxjbh3mpgghpkpy

ORFik: a comprehensive R toolkit for the analysis of translation [article]

Håkon Tjeldnes, Kornel Labun, Yamila N Torres Cleuren, Katarzyna Chyżyńyska, Michał Świrski, Eivind Valen
2021 bioRxiv   pre-print
With the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics, there is a need for back-end functions and streamlined tools for processing  ...  ORFik streamlines the steps to process, analyze, and visualize the different steps of translation with a particular focus on initiation and elongation.  ...  Acknowledgements We would like to thank the Bioconductor core team and community for providing valuable feedback for developing ORFik .  ... 
doi:10.1101/2021.01.16.426936 fatcat:qlyw42tjr5dyzj5kdkyc77zv2a

Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution

Han Fang, Yi-Fei Huang, Aditya Radhakrishnan, Adam Siepel, Gholson J. Lyon, Michael C. Schatz
2018 Cell Systems  
Addressing these issues, we present Scikit-ribo (https://github.com/schatzlab/scikit-ribo), an open-source analysis package for accurate genome-wide A-site prediction and translation efficiency (TE) estimation  ...  New open-source statistical learning software package enables accurate analysis of translational efficiency from Riboseq and RNAseq data.  ...  We also want to thank Rob Patro, Noah Dukler, and Max Doerfel for helpful discussions.  ... 
doi:10.1016/j.cels.2017.12.007 pmid:29361467 pmcid:PMC5832574 fatcat:zc5o7susmzay3cm4kgbthcnkdm

A hitchhiker's guide to expressed sequence tag (EST) analysis

S. H. Nagaraj, R. B. Gasser, S. Ranganathan
2006 Briefings in Bioinformatics  
We provide an overview of the significance of ESTs in the genomic era, their properties and the applications of ESTs.  ...  functional annotation of putative gene products.  ...  Acknowledgements Partial funding from Genetic Technologies Limited and the Australian Research Council (LP0667795), and the award of a Macquarie University research scholarship to S.H.N. is acknowledged  ... 
doi:10.1093/bib/bbl015 pmid:16772268 fatcat:wmumdszmnjalhnw5doqjzicxue

SeMPI: a genome-based secondary metabolite prediction and identification web server

Paul F. Zierep, Natàlia Padilla, Dimitar G. Yonchev, Kiran K. Telukunta, Dennis Klementz, Stefan Günther
2017 Nucleic Acids Research  
The constantly increasing amount of published genomic data provides the opportunity for an efficient identification of gene clusters by genome mining.  ...  Here, we introduce SeMPI, a web server providing a prediction and identification pipeline for natural products synthesized by polyketide synthases of type I modular.  ...  ACKNOWLEDGEMENTS We thank Simon Nicklaus, Michael Kaiser and Lea Purschke for assistance in testing and refinement of the prediction pipeline. Furthermore, we would like to thank Robert A.  ... 
doi:10.1093/nar/gkx289 pmid:28453782 pmcid:PMC5570227 fatcat:kr5tzd2rdjawvax6jjtrmpureq

An improved implementation of codon adaptation index

Xuhua Xia
2007 Evolutionary Bioinformatics  
Codon adaptation index is a widely used index for characterizing gene expression in general and translation efficiency in particular.  ...  The improved CAI can predict protein production better than CAI from other commonly used implementations.  ...  Yao for comments.  ... 
pmid:19461982 pmcid:PMC2684136 fatcat:xngjlh2tkfb5pb5ljta4xdhqre

Clades of huge phages from across Earth's ecosystems

Basem Al-Shayeb, Rohan Sachdeva, Lin-Xing Chen, Fred Ward, Patrick Munk, Audra Devoto, Cindy J. Castelle, Matthew R. Olm, Keith Bouma-Gregson, Yuki Amano, Christine He, Raphaël Méheust (+33 others)
2020 Nature  
The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect  ...  Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors  ...  Although assuming control of initiation may be the most logical step for the redirection of host translation by the phage, improving the efficiency of elongation and termination is necessary for robust  ... 
doi:10.1038/s41586-020-2007-4 pmid:32051592 pmcid:PMC7162821 fatcat:e5y3xqtrbvgd5k4ydlmucvfdgi

An Improved Implementation of Codon Adaptation Index

Xuhua Xia
2007 Evolutionary Bioinformatics  
Codon adaptation index is a widely used index for characterizing gene expression in general and translation effi ciency in particular.  ...  The improved CAI can predict protein production better than CAI from other commonly used implementations.  ...  Yao for comments.  ... 
doi:10.1177/117693430700300028 fatcat:bctnydn3ljdlbjgzkyigydzufy

Fundamental CRISPR-Cas9 tools and current applications in microbial systems

Pingfang Tian, Jia Wang, Xiaolin Shen, Justin Forrest Rey, Qipeng Yuan, Yajun Yan
2017 Synthetic and Systems Biotechnology  
To address these challenges, we came up with strategies that place emphasis on the amelioration of DNA repair efficiency through CRISPR-Cas9-assisted recombineering.  ...  To further characterize the CRISPR technology, we present current applications of these tools in microbial systems, including model-and non-model industrial microorganisms.  ...  The Adli group from University of Virginia developed a web-based tool named CHOP-IT to predict off-targets and to improve guide-RNA design [58] .  ... 
doi:10.1016/j.synbio.2017.08.006 pmid:29318202 pmcid:PMC5655352 fatcat:lk6ircazx5bdnk7chrc5yprkgu

Genetic design automation: engineering fantasy or scientific renewal?

Matthew W. Lux, Brian W. Bramlett, David A. Ball, Jean Peccoud
2012 Trends in Biotechnology  
artificial gene networks has been leveling off since 2005 [11] .  ...  Computer-Aided Design tools for synthetic biology Several groups have been developing Computer-Aided Design (CAD) solutions for synthetic biology [1-10] yet the transcriptional complexity of published  ...  MWL was supported by a fellowship from Science Application International Corporation and by a Department of Defense SMART Scholarship under OSD-T&E (Office of Secretary Defense-Test and Evaluation), Defense-Wide  ... 
doi:10.1016/j.tibtech.2011.09.001 pmid:22001068 pmcid:PMC3779889 fatcat:7wzubr5ewzgjfgsnwplhpotcda

Systems-level analyses identify extensive coupling among gene expression machines

Karolina Maciag, Steven J Altschuler, Michael D Slack, Nevan J Krogan, Andrew Emili, Jack F Greenblatt, Tom Maniatis, Lani F Wu
2006 Molecular Systems Biology  
Our results confirm known coupling among transcription, RNA processing, and export, and predict further coupling with translation and nonsensemediated decay.  ...  Our process identifies and ranks instances of three distinct, biologically motivated motifs, or patterns of coupling among distinct machineries involved in different subprocesses of gene expression.  ...  Yuan, Nicole Francis, and Barbara Wold for critical reading of the manuscript.  ... 
doi:10.1038/msb4100045 pmid:16738550 pmcid:PMC1681477 fatcat:wfhtkbggafbedjycfvqzmzbllq

Computational prediction of the bioactivity potential of proteomes based on expert knowledge

Aitor Blanco-Míguez, Guillermo Blanco, Alberto Gutierrez-Jácome, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço
2019 Journal of Biomedical Informatics  
This has been proven particularly rewarding for microbial cells, for which the majority of proteins are already accessible to analysis through automatic metagenome annotation.  ...  This work introduces a new method for the prediction of the bioactivity potential of proteomes/metaproteomes, supporting the discovery of functionally relevant proteins based on prior knowledge.  ...  Further noteworthy examples of the translational application of the method are antibiotic resistance and foodborne diseases.  ... 
doi:10.1016/j.jbi.2019.103121 pmid:30738947 fatcat:ej4lonhxuzadbakfmr6ghkmayu
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