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ncrna-annotation

separate

Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA, plus the small-RNA-seq boundary for miRNA and the transcript-assembly boundary for lncRNA. Covers the structure-conserved-not-sequence-conserved principle (why BLAST fails), GA-threshold and clan-competition correctness, tRNAscan-SE domain modes and pseudogene flags, rDNA copy-number collapse, and why homology annotation is a recall floor. Use when performing genome-wide ncRNA annotation, choosing the right tool for an RNA class, or interpreting ncRNA counts.

When to use

• genome-wide ncRNA annotation
• choosing the right tool for an RNA class
• interpreting ncRNA counts
• tRNA annotation
• rRNA annotation
• miRNA annotation
• lncRNA annotation
• snoRNA annotation

When not to use

• protein annotation
• BLAST-based structured ncRNA search
• bacterial AMR/CRISPR array detection

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