RNAhub—an automated pipeline to search and align RNA homologs with secondary structure assessment

The complexity in the generation of RNA multiple sequence alignments and assessment of the accuracy of such alignments contributes to the challenges in the utilization of RNA MSAs in diverse integrative methods. RNAhub is a freely available user-friendly web server for a reliable generation of RNA multiple sequence alignents and the detection of the presence of structural RNA utilizing evolutionary information. This web-based tool, developed by the integration of existing computational approaches, takes an RNA sequence as input and automatically retrieves and aligns sequences homologous to the input (query) RNA sequence through an iterative and structure-agnostic approach. Based on the alignment, this tool statistically assesses whether the query RNA sequence has a conserved RNA structure using covariation analysis. The web server allows the user to efficiently search the sequence of interest against carefully curated, ready-to-use genomic databases to produce an MSA. Using this alignment, our tool either detects the presence of a conserved structural RNA, finds evidence against the presence of a conserved structure, or cannot make any assessment due to a lack of sequence diversity in the alignment. The web server is freely available at https://rnahub.org.