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OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes

机译：OpenProt：探索真核编码潜力和蛋白质组的更全面指南

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摘要

Advances in proteomics and sequencing have highlighted many non-annotated open reading frames (ORFs) in eukaryotic genomes. Genome annotations, cornerstones of today's research, mostly rely on protein prior knowledge and on ab initio prediction algorithms. Such algorithms notably enforce an arbitrary criterion of one coding sequence (CDS) per transcript, leading to a substantial underestimation of the coding potential of eukaryotes. Here, we present OpenProt, the first database fully endorsing a polycistronic model of eukaryotic genomes to date. OpenProt contains all possible ORFs longer than 30 codons across 10 species, and cumulates supporting evidence such as protein conservation, translation and expression. OpenProt annotates all known proteins (RefProts), novel predicted isoforms (Isoforms) and novel predicted proteins from alternative ORFs (AltProts). It incorporates cutting-edge algorithms to evaluate protein orthology and re-interrogate publicly available ribosome profiling and mass spectrometry datasets, supporting the annotation of thousands of predicted ORFs. The constantly growing database currently cumulates evidence from 87 ribosome profiling and 114 mass spectrometry studies from several species, tissues and cell lines. All data is freely available and downloadable from a web platform () supporting a genome browser and advanced queries for each species. Thus, OpenProt enables a more comprehensive landscape of eukaryotic genomes’ coding potential.

机译：蛋白质组学和测序技术的进步突出了真核生物基因组中的许多非注释性开放阅读框（ORF）。基因组注释是当今研究的基石，主要依靠蛋白质的先验知识和从头算预测算法。这样的算法尤其是对每个转录本强制采用一个编码序列（CDS）的任意标准，从而导致对真核生物编码潜力的严重低估。在这里，我们介绍OpenProt，这是迄今为止第一个完全支持真核基因组多顺反子模型的数据库。 OpenProt包含10个物种中超过30个密码子的所有可能的ORF，并累积了支持性证据，例如蛋白质保守性，翻译和表达。 OpenProt注释所有已知的蛋白质（RefProts），新的预测同工型（Isoforms）和来自替代ORF（AltProts）的新的预测蛋白。它结合了最先进的算法来评估蛋白质的正交性，并重新审理公开可用的核糖体谱和质谱数据集，从而支持对数千个预测的ORF的注释。这个不断增长的数据库目前收集了来自多个物种，组织和细胞系的87个核糖体谱分析和114个质谱研究的证据。所有数据均可从支持基因组浏览器和每个物种高级查询的Web平台上免费获得和下载。因此，OpenProt可以使真核基因组编码潜力的更全面的认识。

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期刊名称 Nucleic Acids Research
作者
Marie A Brunet; Mylène Brunelle; Jean-François Lucier; Vivian Delcourt; Maxime Levesque; Frédéric Grenier; Sondos Samandi; Sébastien Leblanc; Jean-David Aguilar; Pascal Dufour; Jean-Francois Jacques; Isabelle Fournier; Aida Ouangraoua; Michelle S Scott; François-Michel Boisvert; Xavier Roucou;
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年(卷),期 2019(47),Database issue
年度 2019
页码 D403–D410
总页数 8
原文格式 PDF
正文语种
中图分类分子生物学;
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1. OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes [J] . Marie A Brunet, Mylène Brunelle, Jean-Fran?ois Lucier, Nucleic acids research . 2019,第D1期

机译：OpenProt：探索真核编码潜力和蛋白质组的更全面指南
2. How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource [J] . Marie A. Brunet, Amina M. Lekehal, Xavier Roucou Current Protocols in Bioinformatics . 2020,第1期

机译：如何使用多OMIC OpenProT资源来照亮黑暗蛋白质组
3. Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2-D gel-based approaches [J] . Schmidt F, Dahlmann B, Janek K, Proteomics . 2006,第16期

机译：同位素编码的亲和标签和基于二维凝胶的方法对大鼠肝脏中20S蛋白酶体亚型的全面定量蛋白质组分析
4. Exploring a Synthetic Proteome: Gl obal Analysis of Non-Genetically Encoded Amino Acid Incorporation Across the E. coli Proteome [C] . Hans Rudolf Aerni, Patrick ODonoghue, Svetlana Rogulina, American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics . 2012

机译：探索合成蛋白质组：在大肠杆菌蛋白质组中非遗传编码氨基酸掺入的GL OBAL分析
5. Exploring the Therapeutic Potential of Pseudomonas aeruginosa Exotoxin A and Identifying Eukaryotic Factors Involved in its Intracellular Routing Pathway. [D] . Mohammed, Arshiya Fatima. 2015

机译：探索铜绿假单胞菌外毒素A的治疗潜力，并鉴定涉及其细胞内途径的真核因子。
6. OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes [O] . Marie A Brunet, Jean-François Lucier, Maxime Levesque, 2021

机译：OpenProT 2021：更深的功能诠释了真核基因组的编码潜力
7. ACC/AHA guideline update for perioperative cardiovascular evaluation for noncardiac surgery—executive summary A report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (Committee to Update the 1996 Guidelines on Perioperative Cardiovascular Evaluation for Noncardiac Surgery) 1231When citing this document, the American College of Cardiology and the American Heart Association would appreciate the following citation format: Eagle KA, Berger PB, Calkins H, Chaitman BR, Ewy GA, Fleischmann KE, Fleisher LA, Froehlich JB, Gusberg RJ, Leppo JA, Ryan T, Schlant RC, Winters WL, Jr. ACC/AHA guideline update for perioperative cardiovascular evaluation for noncardiac surgery: executive summary: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (Committee to Update the 1996 Guidelines on Perioperative Cardiovascular Evaluation for Noncardiac Surgery). J Am Coll Cardiol 2002;39:542–53.2The ACC/AHA Task Force on Practice Guidelines makes every effort to avoid any actual or potential conflicts of interest that might arise as a result of an outside relationship or personal interest of a member of the writing panel. Specifically, all members of the writing panel are asked to provide disclosure statements of all such relationships that might be perceived as real or potential conflicts of interest. These statements are reviewed by the parent task force, reported orally to all members of the writing panel at the first meeting, and updated as changes occur.3Single reprints of this document are available by calling 800-253-4636 (US only) or writing the American College of Cardiology, Educational Services, 9111 Old Georgetown Road, Bethesda, MD 20814-1699 (product code 71-0220). This document and the companion full-text guidelines (product code 71-0219), are available on the ACC Web site at www.acc.organd the AHA Web site at www.americanheart.org. To purchase additional reprints (specify version): up to 999 copies, call 800-611-6083 (US only) or fax 413-665-2671; 1000 or more copies, call 214-706-1466, fax 214-691-6342; or E-mail pubauth@heart.org [O] . Eagle Kim A, Berger Peter B, Calkins Hugh, 2002

机译：非心脏手术围术期心血管评估的ACC / AHA指南更新-执行摘要美国心脏病学会/美国心脏协会实践小组指导原则的报告（委员会更新了1996年非心脏外科手术围术期心血管评估指南）1231文件，美国心脏病学会和美国心脏协会将赞赏以下引用格式：Eagle KA，Berger PB，Calkins H，Chaitman BR，Ewy GA，Fleischmann KE，Fleisher LA，Froehlich JB，Gusberg RJ，Leppo JA，Ryan T，Schlant RC，Winters WL，Jr。非心脏手术围手术期心血管评估的ACC / AHA指南更新：摘要：美国心脏病学会/美国心脏协会实践指南工作组的报告（1996年指南更新委员会）非心脏手术围手术期心血管评估的研究）。 J Am Coll Cardiol 2002； 39：542-53.2ACC / AHA实践指南工作组尽一切努力避免由于会员的外部关系或个人利益而引起的任何实际或潜在的利益冲突。写作小组。具体来说，要求写作小组的所有成员提供所有可能被视为实际或潜在利益冲突的关系的披露声明。这些声明由上级工作组审核，在第一次会议上口头报告给写作小组的所有成员，并在发生变化时进行更新。3可以通过致电800-253-4636（仅限美国）或书面获得该文档的单份重印本。美国心脏病学会教育服务学院，马里兰州贝塞斯达，乔治市旧路9111号，邮政编码20814-1699（产品代码71-0220）。该文档和随附的全文指南（产品代码71-0219）可在ACC网站www.acc.organized上获得，也可在AHA网站www.americanheart.org上获得。要购买其他重印本（指定版本）：最多999份，请致电800-611-6083（仅限美国）或传真413-665-2671；否则，请重新发送。 1000或更多副本，请致电214-706-1466，传真214-691-6342;或电子邮件pubauth@heart.org

OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes

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