slncky

slncky identifies, filters, aligns, and prioritizes long non-coding RNAs (lncRNAs) from reconstructed RNA-sequencing and de novo assembled transcriptomes to detect evolutionarily constrained and functionally relevant lncRNA candidates.

Key Features:

• High-Quality LncRNA Filtering: An automated filtering pipeline processes RNA-sequencing data and de novo assembled transcriptomes to produce a high-quality set of putative lncRNAs.
• Evolutionary Constraint Analysis: Analyzes sequence and transcript evolution to prioritize lncRNAs based on evolutionary constraint across species.
• Sensitive Alignment Pipeline: Incorporates a sensitive alignment method tailored for aligning lncRNA loci to detect conserved regions.
• Novel Evolutionary Metrics: Implements new metrics quantifying sequence- and transcript-level evolutionary patterns relevant to lncRNA selection.
• Discovery of Functionally Diverse LncRNA Classes: Enables identification of intergenic lncRNA classes under strong purifying selection on RNA sequence and classes constrained primarily at the regulatory level.

Scientific Applications:

• Prioritization for Experimental Follow-up: Ranks putative lncRNAs for further experimental investigation using conservation and evolutionary metrics.
• Comparative and Evolutionary Analysis: Detects conserved lncRNAs and characterizes selection patterns across species via sequence and transcript evolution analyses.
• Classification of lncRNA Functional Classes: Differentiates lncRNAs exhibiting sequence-level purifying selection from those constrained primarily at the regulatory level.
• Identification of Constrained LncRNAs: Has been used to identify 233 constrained lncRNAs from tens of thousands of annotated transcripts.

Methodology:

Applies an automated filtering pipeline to RNA-sequencing and de novo assembled transcriptomes, uses a sensitive alignment pipeline for lncRNA loci, and analyzes sequence and transcript evolution using novel evolutionary metrics.