Catsnap

Catsnap evaluates the evolutionary conservation of protein isoforms generated by alternative splicing to assess their physiological relevance across species.

Key Features:

• Machine Learning Integration: Catsnap incorporates a machine learning step following an initial database search using provided pairs of protein sequences to improve identification of conserved isoforms.
• Cross-Species Conservation Analysis: It analyzes conservation of experimentally characterized alternative proteins from both plant and animal kingdoms.
• Detection Across AS Types: The tool identifies conserved functional protein isoforms irrespective of the specific type of alternative splicing event that generated them.
• Phylogenetic Insights: Catsnap reports that primary amino acid sequences can be maintained while the types of AS events determining inclusion or exclusion of protein regions vary among plant phylogenetic lineages and are less variable in animals.
• Identification of Functional Hotspots: It highlights hotspots where protein isoforms frequently arise and are likely to carry physiologically relevant functions.

Scientific Applications:

• Evolutionary analysis of alternative splicing: Catsnap enables study of the conservation and evolution of AS events in complex eukaryotic transcriptomes to infer their physiological roles.
• Functional hotspot discovery: It supports identification of protein regions where recurrent isoform generation suggests functional importance and contributes to studies of organismal diversity and adaptation.

Methodology:

The pipeline begins with a database search using pairs of protein sequences provided by the user, followed by a machine learning algorithm that assesses the conservation status of these isoforms across species.