ProGMap

ProGMap maps protein sequences and integrates protein group annotations across multiple databases to assess coherence of protein groups and support functional annotation of newly sequenced proteins.

Key Features:

• Non-redundant dataset: A dataset of over 6.6 million protein sequences mapped to approximately 240,000 distinct protein group descriptions derived from UniProt, RefSeq, Ensembl, COG, KOG, OrthoMCL-DB, HomoloGene, TRIBES, and PIRSF.
• Automated mapping approach: A fast, fully automated mapping method (originally developed for document classification) that constructs a network of links to integrate diverse classification schemes.
• Network integration of classification schemes: Construction of linked networks that combine disparate protein classification schemes to enable cross-database annotation coherence assessment.
• Sequence and identifier mapping: Mapping of sequence identifiers, gene symbols, functional descriptions, amino acid sequences, and nucleotide sequences to protein groups.
• Sequence search capabilities: Incorporation of BLAST similarity search and QuickMatch identity search for identifying similar or identical sequences.

Scientific Applications:

• Annotation reconciliation: Assessing and reconciling conflicting protein group annotations across multiple databases.
• Functional annotation of poorly characterized proteins: Supporting transfer of functional information to partially annotated or uncharacterized proteins by evaluating group coherence.
• High-throughput genomic annotation: Enabling large-scale annotation efforts by mapping high-throughput sequence data to consolidated protein group descriptions.

Methodology:

Uses a fast automated mapping method that constructs a network of links integrating multiple classification schemes; maps sequences from a non-redundant dataset (>6.6 million proteins to ~240,000 group descriptions from UniProt, RefSeq, Ensembl, COG, KOG, OrthoMCL-DB, HomoloGene, TRIBES, and PIRSF); performs BLAST similarity and QuickMatch identity searches.