reCOGnizer

reCOGnizer performs multithreaded domain homology-based annotation of protein sequences using Conserved Domains Database (CDD), NCBIfam, Pfam, Protein Clusters, SMART, TIGRFAM, COG, and KOG to provide detailed functional characterization of large omics and meta-omics datasets.

Key Features:

• Domain homology-based annotation: Performs multithreaded domain homology-based annotation of protein sequences.
• Databases supported: Uses Conserved Domains Database (CDD), NCBIfam, Pfam, Protein Clusters, SMART, TIGRFAM, COG, and KOG for domain detection and functional assignment.
• Annotation details: Retrieves domain names, domain descriptions, and Enzyme Commission (EC) numbers for annotated proteins.
• Scalability: Processes large omics datasets via multithreading to enable high-throughput annotation.
• Integration: Integrates within a suite including UPIMAPI (sequence homology using UniProtKB) and KEGGCharter (visualization within KEGG metabolic pathways).

Scientific Applications:

• Metagenomics: Provides domain-based functional annotations to interpret gene content from metagenomic assemblies.
• Metatranscriptomics: Supports functional characterization of expressed genes by annotating protein sequences derived from metatranscriptomic data.
• Metaproteomics: Enables assignment of domain functions and EC numbers to proteins identified in metaproteomic datasets.
• Microbial ecology and biotechnology: Aids interpretation of microbial functions for ecological studies and biotechnological application development.

Methodology:

Multithreaded processing to annotate protein sequences based on domain homologies.