Since the introduction of the ribosome profiling technique in 2009 its popularity has greatly increased. It is widely used for the comprehensive assessment of gene expression and for studying the mechanisms of regulation at the translational level. As the number of ribosome profiling datasets being produced continues to grow, so too does the need for reliable software that can provide answers to the biological questions it can address. This review describes the computational methods and tools that have been developed to analyze ribosome profiling data at the different stages of the process. It starts with initial routine processing of raw data and follows with more specific tasks such as the identification of translated open reading frames, differential gene expression analysis, or evaluation of local or global codon decoding rates. The review pinpoints challenges associated with each step and explains the ways in which they are currently addressed. In addition it provides a comprehensive, albeit incomplete, list of publicly available software applicable to each step, which may be a beneficial starting point to those unexposed to ribosome profiling analysis. The outline of current challenges in ribosome profiling data analysis may inspire computational biologists to search for novel, potentially superior, solutions that will improve and expand the bioinformatician's toolbox for ribosome profiling data analysis. This article is characterized under: Translation > Ribosome Structure/Function RNA Evolution and Genomics > Computational Analyses of RNA Translation > Translation Mechanisms Translation > Translation Regulation.

中文翻译：

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核糖体分析数据的计算方法。

自从2009年引入核糖体分析技术以来，其受欢迎程度已大大提高。它广泛用于基因表达的综合评估和研究翻译水平的调控机制。随着产生的核糖体图谱数据集的数量持续增长，对可靠软件的需求也随之增加，这些软件可以为它可以解决的生物学问题提供答案。这篇综述描述了在过程的不同阶段分析核糖体谱数据的计算方法和工具。它从原始数据的初始常规处理开始，然后进行更具体的任务，例如识别翻译的开放阅读框，差异基因表达分析或评估局部或全局密码子解码率。该审查指出了与每个步骤相关的挑战，并说明了当前解决这些挑战的方式。此外，它提供了适用于每个步骤的全面的，尽管不完整的，可公开获得的软件列表，对于未进行核糖体谱分析的软件，这可能是一个有益的起点。核糖体图谱分析中当前挑战的概述可能会激发计算生物学家寻找新颖，潜在上乘的解决方案，这些解决方案将改善和扩展生物信息学家用于核糖体图谱数据分析的工具箱。本文的特点是：翻译>核糖体结构/功能RNA进化和基因组学> RNA翻译的计算分析>翻译机制翻译>翻译调控。