RNAhub

RNAhub automates the retrieval and alignment of homologous RNA sequences to facilitate RNA structural and evolutionary studies through covariation analysis.

Key Features:

• Iterative homology search: RNAhub retrieves and aligns sequences homologous to an input query RNA sequence through an iterative and structure-agnostic approach.
• Multiple sequence alignment generation: The tool produces RNA multiple sequence alignments by searching against curated genomic databases.
• Conserved structure detection: RNAhub statistically assesses whether the query RNA sequence has a conserved RNA structure using covariation analysis.
• Structure assessment outcomes: The 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.

Scientific Applications:

• RNA structural biology: RNAhub enables the detection of conserved RNA secondary structures through evolutionary covariation analysis.
• Evolutionary RNA studies: The tool supports investigations of RNA evolution by generating alignments and assessing structural conservation across homologous sequences.
• Integrative RNA analysis: RNAhub provides reliable RNA multiple sequence alignments for use in diverse downstream integrative methods.

Methodology:

RNAhub integrates existing computational approaches to automatically retrieve and align homologous RNA sequences through an iterative and structure-agnostic approach, followed by statistical assessment of conserved RNA structure using covariation analysis.