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Published on: August 15, 2019
ProGMap: an integrated annotation resource for protein orthology
Arnold Kuzniar1, Ke Lin, Ying He
1Laboratory of Bioinformatics, Wageningen University and Research Centre (WUR), Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
Nucleic Acids Research
|June 5, 2009
Summary
ProGMap is a web tool that maps protein sequences across diverse databases, resolving annotation conflicts for researchers. It aids in the accurate annotation of newly sequenced proteins using a unified classification system.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Protein sequence databases utilize varied classification systems, leading to inconsistent annotations, particularly for uncharacterized proteins.
- Accurate protein annotation is crucial for understanding biological functions and advancing research.
Purpose of the Study:
- To introduce ProGMap, a web-tool designed to reconcile conflicting protein annotations across multiple databases.
- To facilitate the annotation of newly sequenced proteins by assessing the coherence of protein groups.
Main Methods:
- ProGMap utilizes a non-redundant dataset of over 6.6 million protein sequences.
- It maps sequences to 240,000 protein group descriptions from various databases (UniProt, RefSeq, Ensembl, etc.).
- A network of links is constructed using an automated mapping approach, integrating diverse classification schemes.
Main Results:
- The tool integrates classification schemes from multiple protein databases.
- It provides a unified view of protein group mappings, enhancing annotation consistency.
- Querying is possible via sequence identifiers, gene symbols, protein functions, or nucleotide/amino acid sequences.
Conclusions:
- ProGMap offers a valuable resource for researchers and database annotators dealing with protein annotation discrepancies.
- It supports high-throughput methodologies by providing coherent annotations for partially annotated genomic data.
- The web-tool promotes more reliable protein classification and facilitates biological discovery.
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