@gmod/jbrowse
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JBrowse - client-side genome browser
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{
"description": "D. melanogaster (release 5.15)",
"db_adaptor": "Bio::DB::SeqFeature::Store",
"db_args": { "-dsn": "dbi:mysql:dmel_5_15" },
"TRACK DEFAULTS": {
"class": "feature"
},
"tracks": [
{
"track": "gene",
"key": "Gene Span",
"feature": ["gene"],
"autocomplete": "all",
"class": "feature2",
"category": "Gene Model features",
"urlTemplate": "http://flybase.org/cgi-bin/fbidq.html?{load_id}",
"extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
},
{
"track": "mRNA",
"feature": ["mRNA"],
"autocomplete": "alias",
"subfeatures": true,
"key": "mRNA",
"class": "transcript",
"subfeature_classes": {
"CDS": "transcript-CDS",
"five_prime_UTR": "transcript-five_prime_UTR",
"three_prime_UTR": "transcript-three_prime_UTR"
},
"arrowheadClass": "transcript-arrowhead",
"clientConfig": {
"histScale":5
},
"urlTemplate": "http://flybase.org/cgi-bin/fbidq.html?{load_id}",
"extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
},
{
"track": "chromosome_band",
"feature": ["chromosome_band"],
"autocomplete": "label",
"key": "Cytological band",
"class": "exon",
"category": "Genomic features"
},
{
"track": "tRNA",
"feature": ["tRNA"],
"autocomplete": "all",
"key": "tRNA",
"class": "helix",
"category": "Genomic features"
},
{
"track": "noncodingRNA",
"feature": ["ncRNA", "snoRNA", "snRNA", "miRNA"],
"autocomplete": "all",
"key": "Non coding RNA",
"class": "feature3",
"category": "Genomic features"
},
{
"track": "transposable_element",
"feature": ["transposable_element"],
"autocomplete": "all",
"key": "Natural transposon",
"category": "Genomic features",
"class": "dblhelix"
},
{
"track": "transposable_element_insertion_site",
"feature": ["transposable_element_insertion_site"],
"autocomplete": "all",
"key": "Transgene insertion site",
"class": "triangle hgred",
"category": "Genomic features"
},
{
"track": "orthologFB",
"feature": ["orthologous_to"],
"key": "Ortholog (FlyBase)",
"category": "Similarity: Synteny features"
},
{
"track": "cDNA",
"feature": ["match:sim4_na_gb.dmel", "match:sim4_na_gb.tpa.dmel", "match:sim4tandem_na_gb.dmel", "match:splign_na_cDNA_ncbi"],
"key": "cDNA and Aligned genomic sequences",
"class": "generic_parent",
"subfeatures": true,
"subfeature_classes": {
"match_part": "generic_part_a"
},
"clientConfig": {
"labelScale": 1000000
},
"category": "Genome reagents and data"
},
{
"track": "EST",
"feature": ["match:sim4_na_dbEST.same.dmel", "match:sim4_na_dbEST.diff.dmel", "match:splign_na_dbEST_ncbi", "match:tblastx_masked_na_dbEST.insect"],
"key": "EST",
"class": "generic_parent",
"subfeatures": true,
"subfeature_classes": {
"match_part": "match_part"
},
"clientConfig": {
"labelScale": 1000000
},
"category": "Genome reagents and data"
},
{
"track": "oligo",
"feature": ["oligonucleotide"],
"key": "Oligonucleotides",
"class": "feature4",
"category": "Genome reagents and data"
},
{
"track": "pcr_product",
"feature": ["pcr_product:DGRC-1"],
"key": "amplicons",
"class": "feature",
"category": "Genome reagents and data"
},
{
"track": "BAC",
"feature": ["BAC_cloned_genomic_insert"],
"key": "Tiling BAC",
"class": "feature",
"category": "Genome reagents and data"
},
{
"track": "protein_binding_site",
"feature": ["protein_binding_site"],
"key": "protein binding site",
"class": "feature",
"category": "Mapped features"
},
{
"track": "enhancer",
"feature": ["enhancer"],
"key": "enhancer",
"class": "feature",
"category": "Mapped features"
},
{
"track": "rescue_fragment",
"feature": ["rescue_fragment"],
"key": "rescue fragment",
"class": "feature",
"category": "Mapped features"
},
{
"track": "transposable_element_target_site_duplication",
"feature": ["transposable_element_target_site_duplication"],
"key": "transposable element target site duplication",
"class": "feature",
"category": "Mapped features"
},
{
"track": "regulatory_region",
"feature": ["regulatory_region"],
"key": "regulatory region",
"class": "feature",
"category": "Mapped features"
},
{
"track": "point_mutation",
"feature": ["point_mutation"],
"key": "Mutation: point mutation",
"class": "feature",
"category": "Mapped features"
},
{
"track": "sequence_variant",
"feature": ["sequence_variant"],
"key": "Mutation: sequence variant",
"class": "feature",
"category": "Mapped features"
},
{
"track": "uncharacterized_change_in_nucleotide_sequence",
"feature": ["uncharacterized_change_in_nucleotide_sequence"],
"key": "Mutation: uncharacterized change in nucleotide_sequence",
"class": "feature",
"category": "Mapped features"
},
{
"track": "aberration_junction",
"feature": ["aberration_junction"],
"key": "Mutation: aberration junction",
"class": "feature",
"category": "Mapped features"
},
{
"track": "complex_substitution",
"feature": ["complex_substitution"],
"key": "Mutation: complex substitution ",
"class": "feature",
"category": "Mapped features"
},
{
"track": "deletion",
"feature": ["deletion"],
"key": "Mutation: deletion",
"class": "feature",
"category": "Mapped features"
},
{
"track": "insertion_site",
"feature": ["insertion_site"],
"key": "Mutation: insertion site",
"class": "feature",
"category": "Mapped features"
},
{
"track": "breakpoint",
"feature": ["breakpoint"],
"key": "breakpoint",
"class": "feature"
},
{
"track": "orthologous_region",
"feature": ["orthologous_region"],
"key": "orthologous_region",
"class": "feature"
},
{
"track": "protein",
"feature": ["protein"],
"key": "protein",
"class": "feature"
},
{
"track": "pseudogene",
"feature": ["pseudogene"],
"key": "pseudogene",
"class": "feature"
},
{
"track": "RNAi_reagent",
"feature": ["RNAi_reagent"],
"key": "RNAi_reagent",
"class": "feature"
}
]
}