<?xml version="1.0"?>
<!DOCTYPE rootElement [
<!ENTITY species SYSTEM "http://dev.medicinalplantgenomics.msu.edu/includes/species_xml.inc.php">
]> 
<site>
    <page name="Home" title="Rice Genome Annotation Project" src="/">
        <page name="Project Overview" title="RGAP - Overview" src="/home/overview"></page>
        <page name="News" title="RGAP - News" src= "/home/news"></page>
        <page name="FAQ" title ="RGAP - FAQ" src="/home/faq"></page>
        <page name="Training" title="RGAP - Training" src="/home/training">
            <page name="Training Opportunities" title="RGAP - Training" src="/home/training/opportunities"></page>
            <page name="Cereal Genomics Lab Module" title="RGAP - Cereal Lab" src="/home/training/cereal"></page>
            <page name="Video Tour" title="RGAP - Video Tour" src="/home/training/video"></page>
        </page>
        <page name="Links" title="RGAP - Links" src="/home/links"></page>
        <page name="Publications" title="RGAP - Publications" src="/home/publications"></page>
        <page name="Contact Us" title="RGAP - Contact Us" src="/home/contacts"></page>
    </page>

    <page name="Rice Gene Annotation" title="RGAP - Gene Annotation" src="/annotation">
        <page name="Pseudomolecules" title="RGAP - Pseudomolecules" src="/annotation/pseudo">
            <page name="Current Pseudomolecules" title="RGAP - Current Pseudomolecules" src="/annotation/pseudo/current"></page>
            <page name="Plant GOSlim Assignment of Rice Protiens" title="RGAP - GOSlim" src="/annotation/pseudo/goslim"></page>
            <page name="Orthologous Groups" title="RGAP - Orhtologous Groups" src="/annotation/pseudo/ortho"></page>
            <page name="Alternatively Spliced Genes" title="RGAP - Alternatively Sliced" src="/annotation/pseudo/altsliced"></page>
            <page name="Pseudomolecule Version Converter" title="RGAP - Version Converter" src="/annotation/pseudo/converter"></page>
            <page name="Redundent and Unmapped BAC/PAC Clones" title="RGAP - Redundent BAC/PAC Clones" src="/annotation/pseudo/clones"></page>
            <page name="Centromeres in the Psuedomolecules" title="RGAP - Centromeres" src="/annotation/pseudo/centromeres"></page>
            <page name="Putative SSRs in the Psuedomolecules" title="RGAP - Putative SSRs" src="/annotation/pseudo/punativessr"></page>
            <page name="Organellar Insertions" title="RGAP - Organellar Insertions" src="/annotation/pseudo/organellar"></page>
            <page name="Segmental Duplication" title="RGAP - Segmental Duplication" src="/annotation/pseudo/segmental"></page>
            <page name="Obsolete Loci" title="RGAP - Obsolete Loci" src="/annotation/pseudo/obsolete"></page>
        </page>
        <page name="In Silico Mapping" title="RGAP - In Silico Mapping" src="/annotation/insilico">
            <page name="Rice Genetic Markers" title="RGAP - Rice Genetic Markers" src="/annotation/insilico/genmarkers"></page>
            <page name="In Silico Mapping of FSTs" title="RGAP - Mapping for FSTs" src="/annotation/insilico/fst"></page>
        </page>
        <page name="Oryza Repeat Database" title="RGAP - Oryza Database" src="/annotation/oryza"></page>
        <page name="Community Annotation" title="RGAP - Community Annotation" src="/annotation/community">
            <page name="Rice Gene Families" title="RGAP - Community Annotation Families" src="/annotation/community/families"></page>
            <page name="Community Annotation Info" title="RGAP - Community Annotation" src="/annotation/community/info"></page>
        </page>
    </page>

    <page name="Rice Gene Expression" title="RGAP - Gene Expression" src="/expression">
        <page name="Anatomy Viewer" title="RGAP - Anatomy Viewer" src="/expression/anatomy"></page>
        <page name="Highly Expressed Genes" title="RGAP - Highly Expressed" src="/expression/highly"></page>
        <page name="Expressed Genes" title="RGAP - Expressed" src="/expression/expressed"></page>
    </page>

    <page name="Analyses/Tools" title="RGAP - Analyses" src="/analyses">
        <page name="Genome Browser" title="RGAP - Genome Browser" src="/analyses/gbrowse"></page>
        <page name="Genome Facts" title="RGAP - Genome Facts" src="/analyses/facts"></page>
        <page name="Gene Nomenclature" title="RGAP - Gene Nomenclature" src="/analyses/nomenclature"></page>
        <page name="Search Functions" title="RGAP - Search Functions" src="/analyses/search">
            <page name="Sequence (BLAST) Search" title="RGAP - BLAST Search" src="/analyses/search/blast"></page>
            <page name="Putative Function Search" title="RGAP - Putative Search" src="/analyses/search/putative"></page>
            <page name="Locus Search" title="RGAP - Locus Search" src="/analyses/search/locus"></page>
            <page name="Domain Search" title="RGAP - Domain Search" src="/analyses/search/domain"></page>
            <page name="Motif Search" title="RGAP - Motif Search" src="/analyses/search/motif"></page>
            <page name="Clone Search" title = "RGAP - Clone Search" src="/analyses/search/clone"></page>
            <page name="Feat Name Search" title = "RGAP - Feat Name Search" src="/analyses/search/featname"></page>
            <page name="tRNA Search" title = "RGAP - tRNA Search" src="/analyses/search/tRNA"></page>
            <page name="GO Retrieval" title="RGAP - GO Retrieval" src="/analyses/search/go"></page>
            <page name="Pseudomolecule Version Converter" title="RGAP - Version Converter" src="/analyses/search/converter"></page>
            <page name="Obsolete Loci" title="RGAP - Obsolete Loci" src="/analyses/search/obsolete"></page>
        </page>
    </page>

    <page name="Downloads" title="RGAP - Downloads" src="/downloads">
        <page name="Genome Annotation Download" title="RGAP - GAD" src="/downloads/gad"></page>
        <page name="Plant Repeat FTP Site" title="RGAP - PlantFTP" src="ftp://ftp.plantbiology.msu.edu/pub/data/TIGR_Plant_Repeats/"></page>
        <page name="Pseudomolecule FTP Site" title="RGAP - PsuedoFTP" src="ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/"></page>
    </page>
</site>
