domains / families / science / ncrna-search

ncrna-search

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Searches for non-coding RNA homologs and classifies RNA families with Infernal covariance models against Rfam, scoring sequence AND secondary-structure conservation jointly. Use when deciding whether a covariance model is the right tool versus BLAST/nhmmer (structured ncRNA versus lncRNA or mature miRNA); choosing the Rfam gathering threshold over a flat E-value; resolving clan overlaps; building and calibrating a custom CM from a structure-annotated alignment; or preferring a family-specialized tool (tRNAscan-SE, barrnap) over a generic Rfam scan.

When to use

• searching sequences for known non-coding RNA families
• classifying RNA families with Infernal covariance models
• deciding between covariance models and BLAST/nhmmer
• choosing Rfam gathering thresholds over flat E-values
• resolving clan overlaps
• building and calibrating custom covariance models
• preferring family-specialized tools over generic Rfam scans

When not to use

• searching lncRNAs without conserved secondary structure
• searching mature miRNAs
• searching primary-sequence-only motifs
• using BLAST or nhmmer for close homologs

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