SLIDR

SLIDR identifies spliced leader (SL) sequences and SL trans-splicing events from RNA-Seq reads and, together with the SLOPPR pipeline, supports genome-wide SL quantification and prediction of eukaryotic operons.

Key Features:

• SL assembly: Assembles putative spliced leaders by analyzing 5’ read tails that are soft-clipped after alignment to a reference genome or transcriptome.
• SL verification: Verifies assembled sequences by searching for sequence motifs characteristic of bona fide SL RNA molecules within corresponding SL RNA genes.
• Novel variant detection: Detects both expected and novel SL variants.
• Read-level quantification: Identifies RNA-Seq reads containing specific 5’ SL sequences to quantify genome-wide SL trans-splicing events.
• Operon prediction: Predicts eukaryotic operons by analyzing distinct patterns of SL trans-splicing across adjacent genes.
• Specialized SL recognition: Recognizes functionally specialized SLs to inform gene regulation analyses.
• Sequencing compatibility: Operates on standard RNA-Seq and emerging full-isoform sequencing protocols and can extract signals from sparse or low-coverage datasets.
• Implementation: Implemented using Bash and R.

Scientific Applications:

• Operon prediction: Identification of SL trans-splicing patterns across adjacent genes to infer eukaryotic operon structure and organization.
• Gene discovery and annotation: Detection of novel SL variants and operons to improve gene model annotation across eukaryotic genomes.
• Evolutionary studies: Comparative analysis of SL trans-splicing diversity and evolution across lineages within Eukarya.

Methodology:

Align reads to a reference genome or transcriptome and analyze soft-clipped 5’ read tails to assemble putative SLs; verify assemblies by searching for SL-characteristic sequence motifs in SL RNA genes; identify reads containing specific 5’ SL sequences to quantify trans-splicing events; analyze SL trans-splicing patterns across adjacent genes to predict operons; implemented in Bash and R.