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However, analyzing and decoding translation information from Ribo-seq data is not trivial. Although there are many existing tools to analyze Ribo-seq data, most of these tools are designed for specific or limited functionalities and an easy-to-use integrated tool to analyze Ribo-seq data is lacking. Fortunately, the small size (26\u201334 nt) of ribosome protected fragments (RPFs) in Ribo-seq and the relatively small amount of sequencing data greatly facilitates the development of such a web platform, which is easy to manipulate for users with or without bioinformatic expertise. Thus, we developed RiboToolkit (http:\/\/rnabioinfor.tch.harvard.edu\/RiboToolkit), a convenient, freely available, web-based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs. Besides, easy-to-use web interfaces were developed to facilitate data analysis and intuitively visualize results. Thus, RiboToolkit will greatly facilitate the study of mRNA translation based on ribosome profiling.<\/jats:p>","DOI":"10.1093\/nar\/gkaa395","type":"journal-article","created":{"date-parts":[[2020,5,15]],"date-time":"2020-05-15T21:40:39Z","timestamp":1589578839000},"page":"W218-W229","source":"Crossref","is-referenced-by-count":79,"title":["RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution"],"prefix":"10.1093","volume":"48","author":[{"given":"Qi","family":"Liu","sequence":"first","affiliation":[{"name":"Stem Cell Program, Division of Hematology\/Oncology, Boston Children's Hospital, Boston, MA 02115, USA"},{"name":"Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA"}]},{"given":"Tanya","family":"Shvarts","sequence":"first","affiliation":[{"name":"Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115, USA"}]},{"given":"Piotr","family":"Sliz","sequence":"first","affiliation":[{"name":"Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA"},{"name":"Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8090-8673","authenticated-orcid":false,"given":"Richard I","family":"Gregory","sequence":"first","affiliation":[{"name":"Stem Cell Program, Division of Hematology\/Oncology, Boston Children's Hospital, Boston, MA 02115, USA"},{"name":"Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"Harvard Initiative for RNA Medicine, Boston, MA 02115, USA"},{"name":"Harvard Stem Cell Institute, Cambridge, MA 02138, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,5,19]]},"reference":[{"key":"2020062614050303600_B1","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science (New York, N.Y.)"},{"key":"2020062614050303600_B2","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1016\/j.tig.2017.08.003","article-title":"Beyond Read-Counts: Ribo-seq data analysis to understand the functions of the transcriptome","volume":"33","author":"Calviello","year":"2017","journal-title":"Trends Genet."},{"key":"2020062614050303600_B3","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/nrm4069","article-title":"Ribosome profiling reveals the what, when, where and how of protein synthesis","volume":"16","author":"Brar","year":"2015","journal-title":"Nat. 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