Searching for similar sequences in a database via BLAST or a similar tool is one of the most common bioinformatics tasks applied in general, and to non-coding RNAs in particular. However, the results of the search might be difficult to interpret due to the presence of partial matches to the database subject sequences. Here, we present rboAnalyzer – a tool that helps with interpreting sequence search result by (1) extending partial matches into plausible full-length subject sequences, (2) predicting homology of RNAs represented by full-length subject sequences to the query RNA, (3) pooling information across homologous RNAs found in the search results and public databases such as Rfam to predict more reliable secondary structures for all matches, and (4) contextualizing the matches by providing the prediction results and other relevant information in a rich graphical output. Using predicted full-length matches improves secondary structure prediction and makes rboAnalyzer robust with regards to identification of homology. The output of the tool should help the user to reliably characterize non-coding RNAs in BLAST output. The usefulness of the rboAnalyzer and its ability to correctly extend partial matches to full-length is demonstrated on known homologous RNAs. To allow the user to use custom databases and search options, rboAnalyzer accepts any search results as a text file in the BLAST format. The main output is an interactive HTML page displaying the computed characteristics and other context of the matches. The output can also be exported in an appropriate sequence and/or secondary structure formats.

通过BLAST或类似工具在数据库中搜索相似序列是普遍应用的最常见的生物信息学任务之一，尤其是对非编码RNA的应用。但是，由于存在与数据库主题序列的部分匹配，因此搜索结果可能难以解释。在这里，我们介绍rboAnalyzer –一种工具，通过以下方法来解释序列搜索结果：（1）将部分匹配扩展为合理的全长主题序列，（2）预测全长主题序列代表的RNA与查询RNA的同源性，（ 3）在搜索结果和公共数据库（例如Rfam）中发现的同源RNA之间汇集信息，以预测所有匹配项的更可靠的二级结构，（4）通过在丰富的图形输出中提供预测结果和其他相关信息，将匹配内容关联起来。使用预测的全长匹配可改善二级结构的预测，并使rboAnalyzer在鉴定同源性方面具有鲁棒性。该工具的输出应帮助用户可靠地表征BLAST输出中的非编码RNA。rboAnalyzer的有用性及其将部分匹配正确延伸至全长的能力在已知的同源RNA上得到了证明。为了允许用户使用自定义数据库和搜索选项，rboAnalyzer接受任何搜索结果作为BLAST格式的文本文件。主要输出是一个交互式HTML页面，显示计算出的特征和匹配的其他上下文。