MyCLADE

MyCLADE annotates protein sequences by applying the MetaCLADE multi-source probabilistic profiling strategy to identify and characterize Pfam domains and domain architectures.

Key Features:

• Multi-Source Domain Annotation: Implements the MetaCLADE strategy to annotate domains using multiple probabilistic profiles for nuanced domain detection.
• Comprehensive Output: Produces detailed domain architectures per sequence, configurable to report targeted domains or clans or all Pfam domains.
• Integration with Databases: Links annotations to Pfam and QuickGO entries to provide domain and clan contextual information.
• Quality Assessment Metrics: Reports E-values, bit-scores, domain-dependent probability scores, and sequence-model logos to evaluate annotation quality.

Scientific Applications:

• Genomic and Metagenomic Functional Profiling: Provides domain-level annotations for functional profiling of genomic and metagenomic sequences.
• Genomics and Proteomics Studies: Supports identification of domain compositions to inform protein function characterization in genomics and proteomics.
• Systems Biology and Evolutionary Analysis: Enables exploration of domain architectures and investigation of evolutionary relationships among proteins.

Methodology:

Annotates input sequences using probabilistic models from Pfam, models domains based on multiple profiles via the MetaCLADE strategy, and integrates Pfam and QuickGO identifiers for annotation enrichment.