SUMMARY Identification of the amino-acid motifs in proteins that are targeted for post-translational modifications (PTMs) is of great importance in understanding regulatory networks. Information about targeted motifs can be derived from mass spectrometry data that identify peptides containing specific PTMs such as phosphorylation, ubiquitylation and acetylation. Comparison of input data against a standardized 'background' set allows identification of over- and under-represented amino acids surrounding the modified site. Conventionally, calculation of targeted motifs assumes a random background distribution of amino acids surrounding the modified position. However, we show that probabilities of amino acids depend on (i) the type of the modification and (ii) their positions relative to the modified site. Thus, software that identifies such over- and under-represented amino acids should make appropriate adjustments for these effects. Here we present a new program, PTM-Logo, that generates representations of these amino acid preferences ('logos') based on position-specific amino-acid probability backgrounds calculated either from user-input data or curated databases. AVAILABILITY AND IMPLEMENTATION PTM-Logo is freely available online at http://sysbio.chula.ac.th/PTMLogo/ or https://hpcwebapps.cit.nih.gov/PTMLogo/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

中文翻译：

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PTM-Logo：一种程序，用于根据特定于位置的背景氨基酸概率生成序列徽标。

发明内容鉴定用于翻译后修饰（PTM）的蛋白质中的氨基酸基序在理解调节网络中非常重要。有关靶向基序的信息可以从质谱数据中获得，该数据可识别包含特定PTM的肽，例如磷酸化，泛素化和乙酰化。将输入数据与标准化的“背景”集进行比较，可以识别修饰位点周围氨基酸的过度表达和表达不足。按照惯例，目标基序的计算假定修饰位置周围的氨基酸是随机背景分布。但是，我们表明氨基酸的概率取决于（i）修饰的类型和（ii）相对于修饰位点的位置。因此，识别这种过量和不足的氨基酸的软件应针对这些影响进行适当的调整。在这里，我们介绍一个新程序PTM-Logo，它基于从用户输入的数据或策展的数据库中计算出的特定于位置的氨基酸概率背景，生成这些氨基酸偏好（“徽标”）的表示。可用性和实现PTM-Logo可从http://sysbio.chula.ac.th/PTMLogo/或https://hpcwebapps.cit.nih.gov/PTMLogo/免费在线获得。补充信息补充数据可从Bioinformatics在线获得。）基于从用户输入的数据或选定的数据库中计算出的位置特定的氨基酸概率背景。可用性和实现PTM-Logo可从http://sysbio.chula.ac.th/PTMLogo/或https://hpcwebapps.cit.nih.gov/PTMLogo/免费在线获得。补充信息补充数据可从Bioinformatics在线获得。）基于从用户输入的数据或选定的数据库中计算出的位置特定的氨基酸概率背景。可用性和实现PTM-Logo可从http://sysbio.chula.ac.th/PTMLogo/或https://hpcwebapps.cit.nih.gov/PTMLogo/免费在线获得。补充信息补充数据可从Bioinformatics在线获得。