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PalmXplore: oil palm gene database.
Nik Shazana Nik Mohd Sanusi1, Rozana Rosli1,2, Mohd Amin Ab Halim1
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia.
Database : the Journal of Biological Databases and Curation
|September 22, 2018
Summary
PalmXplore is a new database for oil palm (Elaeis guineensis) genes, offering a user-friendly system for accessing gene sequences and annotations. It aids research into traits like fatty acid biosynthesis and disease resistance.
Area of Science:
- Agricultural Science
- Bioinformatics
- Genomics
Background:
- Oil palm (Elaeis guineensis) research requires efficient access to gene sequence and annotation data.
- Existing data management systems may lack scalability or user-friendliness for comprehensive genomic analysis.
Purpose of the Study:
- To develop PalmXplore, a scalable data repository and search engine for oil palm genes.
- To facilitate the storage, management, and retrieval of oil palm gene sequences and associated annotations.
- To support research on economically important traits in oil palm.
Main Methods:
- Generated Elaeis guineensis gene set by integrating Fgenesh++ and Seqping prediction pipelines.
- Developed PalmXplore as a data repository with a user-friendly search engine.
- Integrated external annotation databases (Pfam, Gene Ontology, KEGG) and a genome browser (MYPalmViewer).
Main Results:
- PalmXplore provides access to predicted genes, genomic coordinates, and functional annotations.
- Includes data on genes related to fatty acid biosynthesis and disease resistance.
- Offers Basic Local Alignment Search Tool (BLAST) homology search and visualization tools.
Conclusions:
- PalmXplore offers a valuable, freely accessible resource for oil palm genomics research.
- Regular updates ensure the system remains current with new genomic data and features.
- Facilitates efficient data retrieval and analysis for oil palm trait discovery.
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