IsoTV

IsoTV processes short-read as well as Oxford Nanopore (ONT) and Pacific Bio-sciences (PacBio) long-read transcriptome sequencing data to predict and visualize functional features of translated transcript isoforms and assess their potential proteome-level consequences.

Key Features:

• Versatility: Supports short-reads, Oxford Nanopore (ONT), and Pacific Bio-sciences (PacBio) long-reads and can handle single or multiple gene sequences.
• Functional prediction: Incorporates computational tools to predict protein domains, secondary structure, intrinsically disordered regions, and post-translational modification sites of translated isoforms.
• Proteome-level assessment: Assesses potential functional consequences of transcript isoform variation on the proteome.
• Expression and composition summarization: Summarizes gene and isoform expression and transcript composition to enable comparison across conditions.
• Pipeline architecture: Employs a Snakemake-based pipeline architecture to support reproducibility and scalability in processing large datasets.
• Eukaryotic focus: Designed for eukaryotic organisms.

Scientific Applications:

• Cancer biology: Analyzes long-read RNA-seq data to elucidate potential protein isoform functions across cancer cell types.
• Functional genomics and proteomics: Bridges transcriptomic isoform variation and proteome-level functional insights.

Methodology:

Snakemake-based pipeline architecture for reproducible, scalable processing of transcriptome sequencing datasets; designed for eukaryotic organisms.