Novel mRNA Isoform Analysis
Identify and characterize novel peptides from alternative splicing.
The Novel module identifies and characterizes novel peptides that arise from alternative splicing events. These peptides may not be present in canonical protein databases but could have important biological functions.
Key Features
Novel peptide identification from alternative splicing events
BLASTP integration for functional annotation
Comparison with known peptide sequences
Novel peptide characterization and properties
Workflow
Upload FASTA nucleotide sequences (RNA-seq transcripts, long-read sequences, or predicted protein isoforms).
Configure analysis parameters (minimum protein length, genetic code, strand, gene overlap threshold).
Execute ORF finding and select the best open reading frame.
Search candidate genes and select a reference gene for comparison.
Compare novel protein isoform peptides against known reference protein isoforms.
Review peptide specificity and export results.
Novel Isoform Discovery Overview with a three-step pipeline (Upload, Analyze, Compare) and the Novel Transcript Analysis Pipeline for uploading FASTA sequences and configuring analysis parameters.
ORF selection table showing candidate open reading frames ranked by quality score, followed by gene comparison setup where candidate genes are matched for reference comparison.
Novel Isoform Analysis showing a multi-protein-isoform comparative visualization of the novel sequence against reference transcripts, with highlighted protein isoform peptides and their specificity classification (unique, shared).
Output
The module provides:
List of novel peptides with their sequences
ORF quality scores and properties
Multi-protein-isoform comparative visualizations
Peptide specificity analysis (unique vs shared)
Exportable results and figures