FLAMS

FLAMS compares post-translational modification sites to the CPLM and dbPTM databases at the residue level, enabling assessment of novelty and conservation across species in newly generated datasets.

Key Features:

• Residue-level database search: Searches PTM sites against CPLM, the largest dedicated protein lysine modification database, and dbPTM, the most comprehensive general PTM database, at the protein residue level.
• Novelty assessment: Allows researchers to quickly assess the novelty of PTM sites in newly generated datasets.
• Cross-species conservation analysis: Evaluates conservation of modification sites across species to aid functional assessment and prioritization of sites for experimental characterization.
• PTM verification: Enables verification of modifications and assessment of species translation.
• Pipeline integration: Can be integrated into PTM analysis pipelines as a Python3-based command line tool.

Scientific Applications:

• Lysine acylation analysis: Supports identification and comparison of lysine acylation sites and other protein lysine modifications.
• PTM site prioritization: Aids in prioritizing modification sites for further experimental characterization based on novelty and conservation.
• Functional assessment of PTMs: Supports functional assessment of post-translational modification sites through cross-species conservation analysis.
• Large-scale PTM dataset comparison: Enables comparison of new experimental PTM datasets containing hundreds of sites to existing database contents.

Methodology:

FLAMS is implemented in Python3 and performs residue-level comparison of user-provided PTM sites against entries in CPLM and dbPTM databases.