Sircah

Sircah detects and catalogs alternative transcription and splicing events from GFF3 transcript models and spliced alignments to enable analysis of transcriptional variation within gene models.

Key Features:

• Input Flexibility: Accepts GFF3 input representing transcript models from genome-database gene prediction pipelines or from spliced alignments of ESTs and proteins against a genomic sequence.
• Comprehensive Alternative Transcription Detection: Identifies alternative transcription initiation, alternative polyadenylation, alternative 3' and 5' splice-site usage, skipped exons, and retained introns.
• Database Creation: Constructs a detailed, structured database of detected alternative transcription and splicing events for downstream analysis.
• Visualization Capabilities: Generates publication-quality visualizations of detected alternative transcripts in various formats.
• Implementation: Implemented in Python.

Scientific Applications:

• Gene expression regulation studies: Enables analysis of transcriptional diversity and splicing variation within and between gene models.
• Genetic disorder research: Supports investigation of splicing alterations with potential functional implications in disease.
• Evolutionary biology: Facilitates comparative analysis of alternative transcription and splicing across species or lineages.
• Personalized medicine: Provides data on transcript isoform diversity that can inform interpretation of patient-specific splicing variation.

Methodology:

Parses input transcript models or alignments (GFF3) to detect variations in splicing patterns by identifying changes in splice sites, exon inclusion/exclusion, and transcription start/termination points, and compiles detected events into an organized database.