Mercator

Mercator assigns MapMan BIN functional annotations to plant protein and nucleotide sequences using curated reference classifications and protein domain profiles to support genome-scale functional interpretation.

Key Features:

• Functional Annotation Pipeline: Automatically assigns functional annotations using the MapMan BIN ontology tailored for plant 'omics' data.
• Reference Databases: Leverages manually curated reference classifications from Arabidopsis, Chlamydomonas, and rice, reviewed SwissProt annotations from other plant species, and over 2000 protein domain and family profiles from InterPro, CDD, and KOG.
• Parallel Sequence Searches: Performs parallel sequence searches against the comprehensive reference databases and compiles results to compute the most likely MapMan BINs for each query sequence.
• High Accuracy: Produces functional annotations with reported accuracies above 90% when benchmarked against manual annotations.
• Export Formats: Generates mapping files for direct use with MapMan and provides a MapMan-to-GO translation table to export annotations as Gene Ontology (GO) terms.

Scientific Applications:

• Plant functional genomics: Enables genome-scale assignment of functional categories to support interpretation of plant transcriptomes and proteomes.
• Comparative genomics: Facilitates cross-species functional comparison using standardized MapMan BIN classifications and curated reference sets.
• Gene function prediction: Supports inference of gene function from sequence similarity and domain/profile matches against curated databases.
• Pathway and metabolic analysis: Supports characterization and mapping of plant metabolic pathways through BIN-based functional categorization and GO export.

Methodology:

Uses an automated pipeline that assigns MapMan BINs by performing parallel sequence searches against curated reference classifications and reviewed SwissProt annotations, incorporates over 2000 InterPro/CDD/KOG domain and family profiles, compiles search results to compute the most likely MapMan BIN per sequence, and provides a MapMan-to-GO translation table for GO term export.