SLOPPR

SLOPPR identifies RNA-Seq reads containing specific 5’ spliced leader (SL) sequences, quantifies genome-wide SL trans-splicing events, and predicts eukaryotic operons based on SL trans-splicing patterns across adjacent genes.

Key Features:

• SLIDR Pipeline: Assembles putative spliced leader (SL) sequences from 5’ tails of RNA-Seq reads remaining after alignment to a reference genome or transcriptome and verifies them by searching for sequence motifs characteristic of bona fide SL RNA genes.
• SLOPPR Pipeline: Identifies RNA-Seq reads containing specific 5’ SL sequences, quantifies SL trans-splicing genome-wide, and predicts operons by detecting distinct SL trans-splicing patterns across adjacent genes to identify known and novel operonic structures.
• SL variant detection: Detects expected SLs, novel SL variants, and functionally specialized SLs in organisms known for SL trans-splicing such as Caenorhabditis elegans and trypanosomes.
• Low-coverage compatibility: Extracts SL and operon information from sparse or low-coverage RNA-Seq datasets.

Scientific Applications:

• Evolutionary analysis of SL trans-splicing: Comparative and evolutionary studies of SL trans-splicing mechanisms across Eukarya.
• Operon discovery and annotation: Discovery and annotation of eukaryotic operons, including identification of novel operonic structures.
• Gene discovery and genome annotation: Enhances gene discovery and annotation by resolving polycistronic pre-mRNAs into monocistronic transcripts using SL trans-splicing evidence.
• Model organism validation: Validation and benchmarking of SL and operon predictions in organisms with established SL trans-splicing such as Caenorhabditis elegans and trypanosomes.

Methodology:

Implemented in Bash and R, the pipelines use RNA-Seq read alignment to a reference genome or transcriptome, assemble 5’ read tails to reconstruct putative SL sequences, search for SL RNA–characteristic sequence motifs within corresponding genes, identify reads containing specific 5’ SL sequences, quantify SL trans-splicing events genome-wide, and predict operons based on SL trans-splicing patterns across adjacent genes, with applicability to sparse or low-coverage datasets.