Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada.
PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada.
Nucleic Acids Res. 2021 Jan 8;49(D1):D380-D388. doi: 10.1093/nar/gkaa1036.
OpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides a deeper annotation of open reading frames (ORFs) while mining experimental data for supporting evidence using cutting-edge algorithms. This update presents the major improvements since the initial release of OpenProt. All species support recent NCBI RefSeq and Ensembl annotations, with changes in annotations being reported in OpenProt. Using the 131 ribosome profiling datasets re-analysed by OpenProt to date, non-AUG initiation starts are reported alongside a confidence score of the initiating codon. From the 177 mass spectrometry datasets re-analysed by OpenProt to date, the unicity of the detected peptides is controlled at each implementation. Furthermore, to guide the users, detectability statistics and protein relationships (isoforms) are now reported for each protein. Finally, to foster access to deeper ORF annotation independently of one's bioinformatics skills or computational resources, OpenProt now offers a data analysis platform. Users can submit their dataset for analysis and receive the results from the analysis by OpenProt. All data on OpenProt are freely available and downloadable for each species, the release-based format ensuring a continuous access to the data. Thus, OpenProt enables a more comprehensive annotation of eukaryotic genomes and fosters functional proteomic discoveries.
OpenProt（www.openprot.org）是第一个支持真核生物基因组多顺反子注释模型的蛋白质组学资源。它通过使用最先进的算法挖掘实验数据来提供更深入的开放阅读框（ORF）注释，并为支持证据提供了更深入的注释。此更新介绍了自 OpenProt 初始发布以来的主要改进。所有物种都支持最新的 NCBI RefSeq 和 Ensembl 注释，OpenProt 会报告注释的更改。使用 OpenProt 迄今为止重新分析的 131 个核糖体分析数据集，报告了非 AUG 起始的起始密码子及其起始密码子置信度评分。从 OpenProt 迄今为止重新分析的 177 个质谱数据集，在每个实现中都控制了检测到的肽的唯一性。此外，为了指导用户，现在为每个蛋白质报告了可检测性统计信息和蛋白质关系（同工型）。最后，为了促进在不依赖于用户生物信息学技能或计算资源的情况下访问更深入的 ORF 注释，OpenProt 现在提供了一个数据分析平台。用户可以提交他们的数据集进行分析，并从 OpenProt 接收分析结果。OpenProt 上的所有数据都可免费获得，并且可以下载每个物种的数据，基于版本的格式确保了对数据的持续访问。因此，OpenProt 能够更全面地注释真核生物基因组，并促进功能蛋白质组学的发现。
