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test-comparative.html
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test-comparative.html
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<!DOCTYPE html>
<html>
<head>
<style>
</style>
<title>Human GRCh37 :: Dalliance</title>
<script language="javascript" src="ode_modules/dalliance/node_modules/es6-promise/dist/promise-0.1.1.js"></script>
<script language="javascript" src="node_modules/dalliance/js/bam.js"></script>
<script language="javascript" src="node_modules/dalliance/js/bigwig.js"></script>
<script language="javascript" src="node_modules/dalliance/js/das.js"></script>
<script language="javascript" src="node_modules/dalliance/js/spans.js"></script>
<script language="javascript" src="node_modules/dalliance/js/utils.js"></script>
<script language="javascript" src="node_modules/dalliance/js/cbrowser.js"></script>
<script language="javascript" src="node_modules/dalliance/js/feature-popup.js"></script>
<script language="javascript" src="node_modules/dalliance/js/tier.js"></script>
<script language="javascript" src="node_modules/dalliance/js/features.js"></script>
<script language="javascript" src="node_modules/dalliance/js/color.js"></script>
<script language="javascript" src="node_modules/dalliance/js/feature-draw.js"></script>
<script language="javascript" src="node_modules/dalliance/js/sequence-draw.js"></script>
<script language="javascript" src="node_modules/dalliance/js/domui.js"></script>
<script language="javascript" src="node_modules/dalliance/js/track-adder.js"></script>
<script language="javascript" src="node_modules/dalliance/js/chainset.js"></script>
<script language="javascript" src="node_modules/dalliance/js/version.js"></script>
<script language="javascript" src="node_modules/dalliance/js/sha1.js"></script>
<script language="javascript" src="node_modules/dalliance/js/sample.js"></script>
<script language="javascript" src="node_modules/dalliance/js/kspace.js"></script>
<script language="javascript" src="node_modules/dalliance/js/bin.js"></script>
<script language="javascript" src="node_modules/dalliance/js/twoBit.js"></script>
<script language="javascript" src="node_modules/dalliance/js/thub.js"></script>
<script language="javascript" src="node_modules/dalliance/js/svg-export.js"></script>
<script language="javascript" src="node_modules/dalliance/node_modules/jszlib/js/inflate.js"></script>
<script language="javascript" src="node_modules/dalliance/js/browser-ui.js"></script>
<script language="javascript" src="node_modules/dalliance/js/glyphs.js"></script>
<script language="javascript" src="node_modules/dalliance/js/session.js"></script>
<script language="javascript" src="node_modules/dalliance/js/jbjson.js"></script>
<script language="javascript" src="node_modules/dalliance/js/sourceadapters.js"></script>
<script language="javascript" src="node_modules/dalliance/polyfills/html5slider.js"></script>
<script language="javascript" src="node_modules/dalliance/js/ensembljson.js"></script>
<script language="javascript" src="node_modules/dalliance/js/overlay.js"></script>
<script language="javascript" src="node_modules/dalliance/js/tier-actions.js"></script>
<script language="javascript" src="node_modules/dalliance/js/tier-edit.js"></script>
<script language="javascript" src="node_modules/dalliance/js/search.js"></script>
<script language="javascript" src="node_modules/dalliance/js/tabix.js"></script>
<script language="javascript" src="node_modules/dalliance/js/tabix-source.js"></script>
<script language="javascript" src="node_modules/dalliance/js/bigtab.js"></script>
<script language="javascript" src="node_modules/dalliance/js/memstore.js"></script>
<script language="javascript" src="node_modules/dalliance/js/vcf.js"></script>
<script language="javascript" src="node_modules/dalliance/js/bedwig.js"></script>
<script language="javascript" src="node_modules/dalliance/js/probe.js"></script>
<script language="javascript" src="node_modules/dalliance/js/trix.js"></script>
<script language="javascript" src="node_modules/dalliance/js/export-ui.js"></script>
<script language="javascript" src="node_modules/dalliance/js/export-config.js"></script>
<script language="javascript" src="node_modules/dalliance/js/export-image.js"></script>
<script language="javascript" src="node_modules/dalliance/js/svg-utils.js"></script>
<script language="javascript" src="node_modules/dalliance/js/numformats.js"></script>
<script language="javascript" src="node_modules/dalliance/js/cigar.js"></script>
<script language="javascript" src="node_modules/dalliance/js/lh3utils.js"></script>
<script language="javascript" src="comparative.js"></script>
<script language="javascript">
var mouse = new Browser({
chr: '5',
viewStart: 150492648,
viewEnd: 150626627,
cookieKey: 'mouse38',
pageName: 'mouseHolder',
coordSystem: {
speciesName: 'Mouse',
taxon: 10090,
auth: 'GRCm',
version: 38,
ucscName: 'mm10'
},
chains: {
mm9ToMm10: new Chainset('http://www.derkholm.net:8080/das/mm9ToMm10/', 'NCBIM37', 'GRCm38',
{
speciesName: 'Mouse',
taxon: 10090,
auth: 'NCBIM',
version: 37,
ucscName: 'mm9'
}),
hg19ToMm10: {
coords: {
speciesName: 'Human',
taxon: 9606,
auth: 'GRCh',
version: '37',
ucscName: 'hg19',
},
uri: 'http://www.biodalliance.org/datasets/hg19ToMm10.bb',
type: 'bigbed'
}
},
sources: [{name: 'Genome',
twoBitURI: 'http://www.biodalliance.org/datasets/GRCm38/mm10.2bit',
desc: 'Mouse reference genome build GRCm38',
tier_type: 'sequence',
provides_entrypoints: true}
,{name: 'Genes',
desc: 'Gene structures from GENCODE M2',
bwgURI: 'http://www.biodalliance.org/datasets/GRCm38/gencodeM2.bb',
stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode.xml',
collapseSuperGroups: true,
trixURI: 'http://www.biodalliance.org/datasets/GRCm38/gencodeM2.ix'}
,{name: 'Repeats',
desc: 'Repeat annotation from UCSC',
bwgURI: 'http://www.biodalliance.org/datasets/GRCm38/repeats.bb',
stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats2.xml'}],
uiPrefix: 'http://www.biodalliance.org/dev/',
disablePoweredBy: false,
toolbarBelow: true,
});
var human = new Browser({
chr: '13',
viewStart: 32864490,
viewEnd: 32998468,
cookieKey: 'human-grc_h37-offline4',
pageName: 'humanHolder',
coordSystem: {
speciesName: 'Human',
taxon: 9606,
auth: 'GRCh',
version: '37',
ucscName: 'hg19',
},
chains: {
mm10ToHg19: {
coords: {
speciesName: 'Mouse',
taxon: 10090,
auth: 'GRCm',
version: 38
},
uri: 'http://www.biodalliance.org/datasets/mm10ToHg19.bb',
type: 'bigbed'
}
},
sources: [{name: 'Genome',
desc: 'Human reference genome build GRCh37',
twoBitURI: 'http://www.biodalliance.org/datasets/hg19.2bit',
provides_entrypoints: true,
disabled: false,
pinned: true
},
{name: 'GENCODE',
bwgURI: 'http://www.biodalliance.org/datasets/gencode.bb',
stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode.xml',
collapseSuperGroups: true,
trixURI: 'http://www.biodalliance.org/datasets/geneIndex.ix'},
{name: 'Repeats',
desc: 'Repeat annotation from Ensembl 59',
bwgURI: 'http://www.biodalliance.org/datasets/repeats.bb',
stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats.xml'}
],
setDocumentTitle: true,
uiPrefix: 'http://www.biodalliance.org/dev/',
fullScreen: true,
maxWorkers: 0,
maxViewWidth: 1000000,
noRegistryTabs: true,
defaultHighlightFill: 'yellow',
defaultHighlightAlpha: 0.15,
toolbarBelow: false,
disablePoweredBy: true,
browserLinks: {
Ensembl: 'http://ncbi36.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr${chr}:${start}-${end}',
Sequence: 'http://www.derkholm.net:8080/das/hg19comp/sequence?segment=${chr}:${start},${end}'
}
});
human.addInitListener(function() {
var compcan = document.getElementById('comparison');
human.addViewListener(function() {
refreshComparative(compcan, human, 'mm10ToHg19', mouse, 'hg19ToMm10');
});
mouse.addViewListener(function() {
refreshComparative(compcan, human, 'mm10ToHg19', mouse, 'hg19ToMm10');
});
compcan.addEventListener('click', function(ev) {
syncComparative(human, mouse, 'mm10ToHg19');
}, false);
});
</script>
</head>
<body>
<a href='http://www.ensembl.org/' id='enslink' target='_newtab' style='display: none'>Link to Ensembl</a>
<div id='humanHolder'>Dalliance here...</div>
<canvas id='comparison' width='800' height='200'></canvas>
<div id='mouseHolder'>Dalliance genome browser goes here. Unless you have an ancient web browser or something.</div>
</body>
</html>