TCMPG

TCMPG aggregates genome sequences and associated herbal-medicine data from medicinal plants sequenced by high-throughput sequencing technologies to enable comparative and functional genomic analyses of Traditional Chinese Medicine (TCM) species.

Key Features:

• Data repository: Comprises data for 160 medicinal plants, 195 genome sequences, and 255 herbal medicines.
• Data integration: Integrates species, genome, and herbal-medicine datasets to link genomic information with TCM resources.
• BLAST: BLAST for identifying orthologs across plant species to support comparative genomics.
• SSR Finder: SSR Finder for detection of simple sequence repeats (SSRs) as genetic markers.
• JBrowse: JBrowse for browsing and visualizing genomic sequences and regions.
• Synteny Viewer: Synteny Viewer to display syntenic blocks between two genomes for studies of genome evolution and conservation.
• HmmSearch: HmmSearch for identification of protein domains within genomic data to aid gene function annotation.

Scientific Applications:

• Comparative genomics: Identification of orthologs and syntenic blocks to compare genomes across medicinal plant species.
• Marker development and breeding: SSR detection to develop genetic markers useful in genetic research and breeding programs.
• Gene function annotation: Protein domain identification via HmmSearch to support functional annotation and regulation studies.
• Genome visualization: Visualization of genomic regions and annotations using JBrowse.
• TCM genomics research: Integration of genome and herbal-medicine data to investigate genetic bases of Traditional Chinese Medicine species.

Methodology:

Integration of genome and herbal-medicine datasets and the application of BLAST, SSR Finder, JBrowse, Synteny Viewer, and HmmSearch for ortholog detection, SSR identification, genomic visualization, synteny display, and protein domain identification.