ProteoDisco：一种灵活的 R 方法，用于生成定制的蛋白质数据库，以扩展蛋白质组学研究中新的和变体蛋白质的搜索空间。
ProteoDisco: a flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies.
机构信息
Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands.
Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands.
出版信息
Bioinformatics. 2022 Feb 7;38(5):1437-1439. doi: 10.1093/bioinformatics/btab809.
SUMMARY
We present an R-based open-source software termed ProteoDisco that allows for flexible incorporation of genomic variants, fusion genes and (aberrant) transcriptomic variants from standardized formats into protein variant sequences. ProteoDisco allows for a flexible step-by-step workflow allowing for in-depth customization to suit a myriad of research approaches in the field of proteogenomics, on all organisms for which a reference genome and transcript annotations are available.
AVAILABILITY AND IMPLEMENTATION
ProteoDisco (R package version ≥ 1.0.0) is available on Bioconductor at https://doi.org/doi:10.18129/B9.bioc.ProteoDisco and from https://github.com/ErasmusMC-CCBC/ProteoDisco/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
我们提出了一种基于 R 的开源软件 ProteoDisco，它允许将基因组变异、融合基因和（异常）转录组变异从标准化格式灵活地合并到蛋白质变异序列中。ProteoDisco 允许灵活的逐步工作流程，允许根据需要进行深入定制，以适应蛋白质基因组学领域的各种研究方法，适用于所有具有参考基因组和转录注释的生物体。
可用性和实现
ProteoDisco（R 包版本≥1.0.0）可在 Bioconductor 上获得，网址为 https://doi.org/doi:10.18129/B9.bioc.ProteoDisco，也可从 https://github.com/ErasmusMC-CCBC/ProteoDisco/ 获得。
补充信息
补充数据可在 Bioinformatics 在线获得。
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