Abstract
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.
Highlights
The output of a BLAST (Camacho et al, 2009) search is a list of hits of the query sequence in the search database that are called high-scoring pairs (HSPs)
The score is a measure of the homology of the subject RNAs to the query RNA in terms of similarity of their sequences represented by their extended matches and their potential secondary structure
The default set-up for rboAnalyzer includes “locarna” method for extension of partial matches and three methods for the secondary structure prediction, RNAfold, TurboFold, and rfam-Rc
Summary
The output of a BLAST (Camacho et al, 2009) search is a list of hits of the query sequence in the search database that are called high-scoring pairs (HSPs). The rboAnalyzer pipeline extends partial or otherwise imperfect matches to the length of the query sequence and computes its secondary structure and a homology to the query RNA.
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