ELMMatcher

ELMMatcher maps Eucaryotic Linear Motifs (ELMs) onto query sequences to identify short, non-globular functional motifs involved in cell compartment targeting, protein-protein interactions, and post-translational modifications such as phosphorylation, acetylation, and glycosylation.

Key Features:

• Comprehensive Motif Database: Uses the ELM server, a curated repository of short linear peptide motifs, as the reference motif database.
• Sequence Comparison: Compares query sequences against the database of known ELMs to detect motif matches.
• Logical Filtering System: Applies Cell Compartment, Globular Domain Clash, and Taxonomic Range filters to focus on biologically relevant non-globular regions.
• Significance Assessment: Employs filtering to reduce false positives, reportedly by an order of magnitude or more in favorable cases.

Scientific Applications:

• Multidomain Protein Analysis: Identifies functional short motifs within multidomain proteins to aid annotation of individual sequence segments.
• Protein Functionality: Elucidates how short motifs contribute to protein function through interactions and regulatory events.
• Post-translational Modifications: Maps candidate sites for phosphorylation, acetylation, glycosylation, and other modifications.
• Cellular Localization: Assesses motifs that influence targeting of proteins to specific cellular compartments.

Methodology:

Query sequences are compared against a database of known ELMs and logical filters (Cell Compartment, Globular Domain Clash, Taxonomic Range) are applied during this comparison to retain biologically relevant, non-redundant matches.