surfaltr

surfaltr benchmarks surface protein isoforms and predicts transmembrane (TM) topology within R/Bioconductor to assess effects of alternative splicing on subcellular localization and the druggable proteome relevant to tissue-specific delivery of oligonucleotide and cell-based therapeutics.

Key Features:

• Isoform pairing: Pairs input isoforms with the known principal isoform of the gene for comparative analysis of sequence and topology differences.
• TM topology prediction: Predicts transmembrane (TM) topology for user-provided isoforms to inform subcellular localization and membrane topology changes due to alternative splicing.
• Graphical output: Generates customizable graphical representations of predicted TM topologies for interpretation and presentation.
• Prioritization metrics: Implements three distinct ranking metrics to prioritize isoform pairs based on topological diversity.
• Protein alignment functions: Provides protein alignment routines to compare isoform sequences and principal proteins for detailed structural and sequence analysis.

Scientific Applications:

• Tissue-specific isoform discovery and evaluation: Supports discovery and evaluation of tissue-specific alternatively spliced or novel surface protein isoforms from multiomic studies.
• Mouse retina isoform analysis: Has been applied to evaluate mouse retina-specific isoforms as demonstrated in Ray et al., 2020.

Methodology:

Integrates user-input isoform data with existing genomic information, leverages bioinformatic algorithms to predict transmembrane (TM) topology, and applies analytical metrics and visualization routines to prioritize and display isoform topological diversity.