ProTeus

ProTeus identifies short linear signatures at protein termini using a position-based search methodology to associate terminal motifs with functional annotations and evolutionary analysis, including links to Gene Ontology (GO) terms.

Key Features:

• Position-based search methodology: Searches for short linear signatures based on their relative positions at protein termini.
• Signature group (SIG) collection and definition: Groups signatures into SIGs defined by their relative positions at protein termini.
• Statistical evaluation and refinement: Applies rigorous statistical evaluation and threshold-based refinement to retain significant SIGs.
• Terminal-conserved similarity isolation: Identifies SIGs that represent protein sets with minimal overall sequence similarity except for conserved terminal similarities.
• Curated SIG archive and GO correspondence: Archives curated SIGs and organizes them according to correspondence with functional annotations from external databases such as Gene Ontology (GO).
• Search and visualization for evaluation and discovery: Provides search and visualization capabilities to evaluate SIG quality and to detect new terminal signatures in novel sequences.

Scientific Applications:

• Functional annotation prediction: Associates terminal signatures with Gene Ontology (GO) annotations to support prediction of protein function.
• Comparative proteomics studies: Enables comparative analyses of terminal signature distributions across proteomes.
• Evolutionary biology research: Supports studies of protein evolution by identifying conserved terminal motifs across divergent proteins.

Methodology:

Position-based search for short linear terminal signatures; collection of signature groups (SIGs) defined by relative termini positions; statistical evaluation and threshold-based refinement to select significant SIGs; archival of curated SIGs with correspondence to Gene Ontology (GO) annotations; search and visualization to evaluate SIG quality and detect signatures in novel sequences.