PhyloFacts FAT-CAT

PhyloFacts FAT-CAT places protein sequences into phylogenomic orthology groups and derives functional annotations using subtree hidden Markov models to identify orthologs and distinguish paralogs across diverse taxa.

Key Features:

• Subtree Hidden Markov Model-Based Placement: Uses subtree hidden Markov models to score and place protein sequences into phylogenomic groups within the PhyloFacts database.
• Functional Annotation with Confidence Scores: Derives functional annotations for input sequences and provides associated confidence scores.
• Broad Taxonomic Coverage: Leverages the PhyloFacts database containing over 7.3 million proteins spanning the Tree of Life.
• Pipeline Parameter Presets: Implements four preset analysis pipelines tailored for different sequence types, including partial sequences and sequences with promiscuous domains.
• Robustness to Promiscuous Domains: Applies methods that enable high precision in distinguishing orthologs and paralogs for proteins with promiscuous domains.
• Input Size Support: Accepts protein sequences up to 2000 amino acids for placement and annotation.

Scientific Applications:

• Orthology Inference: Identification of orthologs and discrimination of paralogs for evolutionary and comparative analyses.
• Protein Functional Annotation: Assignment of putative functions to proteins via placement into phylogenomic orthology groups with confidence metrics.
• Comparative Genomics and Evolutionary Biology: Analysis of protein family evolution and functional conservation across microbial, plant, and animal proteins.

Methodology:

Input protein sequences (up to 2000 amino acids) are scored and placed into phylogenomic orthology groups from the PhyloFacts database using subtree hidden Markov models; functional annotations and confidence scores are derived from the assigned phylogenomic groups; four preset pipelines address full-length, partial, and promiscuous-domain sequences.