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2021-05-27
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HTTP/1.1 200 OKDate: Fri, 09 Jan 2026 06:18:27 GMTContent-Type: text/html; charsetUTF-8Transfer-Encoding: chunkedConnection: keep-aliveServer: Apache/2.4.46 () OpenSSL/1.0.2k-fips PHP/5.6.40X-Powered-By: PHP/5.6.40Set-Cookie: PHPSESSID8djomcnvub85u6qo83nfmeo576; path/Expires: Thu, 19 Nov 1981 08:52:00 GMTCache-Control: no-store, no-cache, must-revalidate, post-check0, pre-check0Pragma: no-cache !DOCTYPE html PUBLIC -//W3C//DTD XHTML 1.0 Transitional//EN http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd>html xmlnshttp://www.w3.org/1999/xhtml>head> title>MSeqDR ~ Accelerating Genomic Discovery in Mitochondrial Diseases/title> meta namedescription contentMSeqDR Mitochondrial Disease pathogenic mutation variant /> meta namedescription contentThis is MSeqDR.org, the mtDNA and mitochondrial disease tool and data resource, using NGS and clinical data to do exome, genome and pathogenic variant interpretation.> meta propertyog:title contentMSeqDR.org ~ Accelerating Genomic Discovery in Mitochondrial Diseases /> meta propertyog:description contentThis is MSeqDR.org, the mtDNA and mitochondrial disease tool and data resource! /> meta propertyog:url contenthttps://MSeqDR.org /> meta propertyog:image contenthttps://localhost/mseqdr/images/logo_mseqdr.png /> meta namekeywords content MSeqDR Mitochondrial disease pathogenic mutation variant /> !-- script typetext/javascript src./js/jquery-1.11.1.min.js>/script> -->script srcjs/jquery.2.2.0.min.js>/script>link relstylesheet hrefjs/slimmenu.css typetext/css>script srcjs/jquery.slimmenu.min.js>/script>script srcjs/sharetastic.js>/script>link relstylesheet hrefjs/sharetastic.css/>style>body { } #tool { display: none; } .tool_a:hover #tool { display:block; } .tool_a:hover #tool_img { display: none; } #lsdb { display: none; } .lsdb_a:hover #lsdb { display:block; } .lsdb_a:hover #lsdb_img { display: none; } #submit { display: none; } .submit_a:hover #submit { display:block; } .submit_a:hover #submit_img { display: none; } #gemapp { display: none; } .gemapp_a:hover #gemapp { display:block; } .gemapp_a:hover #gemapp_img { display: none; } /style>style> .annotationtable table, .annotationtable th, .annotationtable td { border: 1px solid blue; margin: 2px; min-width: 200px; font-family:sans-serif; font-size:10pt; font-color:white; color:solid blue; background-color:lightblue; background-image: url(images/1.png); } code { white-space: normal; }/style> /head>body >link relstylesheet hrefcss/style_navarrod.css typetext/css />script srcjs/jquery.slimmenu.min.js>/script> link relstylesheet href./js/jquery-ui-1.10.3/d1.css> link relstylesheet href./js/jquery-ui-1.10.3/themes/base/jquery.ui.all.css>script typetext/javascript srcjs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.min.js>/script>script srcjs/jquery-ui-1.10.3/ui/minified/jquery.ui.core.min.js>/script>script srcjs/jquery-ui-1.10.3/ui/minified/jquery.ui.widget.min.js>/script>script srcjs/jquery-ui-1.10.3/ui/minified/jquery.ui.position.min.js>/script>script srcjs/jquery-ui-1.10.3/ui/minified/jquery.ui.autocomplete.min.js>/script>link relstylesheet hrefjs/jquery-ui-1.10.4/css/smoothness/jquery-ui.css>script typetext/javascript src./js/ac.js>/script>style>#keyword { width: 50px; font-size: 1em;}#results { display: none; width: 240px; display: absolute; border: 1px solid #c0c0c0;}#results .item { padding: 3px; font-family: Helvetica; border-bottom: 1px solid #c0c0c0; font-size: 9pt;}#results .item:last-child { border-bottom: 0px;}#results .item:hover { background-color: #f2f2f2; cursor: pointer;}/style>!-- LSHEN 2014-07-23: Fixing these ->!-- Causing Real Ajax Uploader Conflict: script srcjs/jquery-ui-1.10.4/js/jquery-1.10.2.js>/script> -->!-- Causing Real Ajax Uploader Conflict: script typetext/javascript srcjs/jquery-1.11.1.min.js>/script> -->!-- Causing Real Ajax Uploader Conflict: script src./js/jquery.js>/script> --> div idwhole_web>div idhead>div idhead_menu_bar> div idhead_menu > ul> li> a hrefindex.php>About/a> ul> li>a hrefnews.php>News/a>/li> li>a hrefpeople.php>Team/a>/li> li>a hrefhttps://projectreporter.nih.gov/project_info_description.cfm?aid9411950 target_blank>U24 Grant/a>/li> li>a hrefdocumentation.php>Documentation/a>/li> li>a hreftutorial.php>Tutorial/a>/li> li>a hrefumdf17.php>UMDF17 Workshop/a>/li> li>a hrefhttps://mseqdr.org/doc/MSeqDR_Brief_Intro_Tutorial_UMDF_St_Louis_20170310.html>UMDF17 Regional Symposia St Louis/a>/li> li>a hrefumdf16.php>UMDF16 Workshop/a>/li> li>a hrefumdf15.php>UMDF15 Workshop/a>/li> li>a hrefsimd.php>SIMD15 Workshop/a>/li> li>a hrefzone.php target_blank titleProject-specific wiki, forum discussion, chat room, cloud style large file sharing, task, agenda. Create our private project zone.>Collaboration Zone/a>/li> li>a hrefmitobook.php>Book: Mitochondrial Disease Genes Compendium /a>/li> li>a hreffeedback.php>Contact & Feedback/a>/li> /ul> /li> !-- li>a hrefgbrowse_bridge.php>GBrowse/a> /li> --> li>a hrefmb.php?urlindex.php>MSeqDR-LSDB/a> ul> li>a hrefmb.php?urlgenes.php>Genes View /a> /li> li>a hrefmb.php?urltranscripts.php>Transcripts/a>/li> li>a hrefmb.php?urldiseases.php>Mitochondrial Disease /a>span stylefont-size:10.0pt;color:yellow;>a hrefmb.php?urldiseases.php?create>img srcimages/tree_expand.png width12px height12px altcreate />/a>/span>/li> li>a hrefmb.php?urlvariants.php>Genomic Variants /a>span stylefont-size:10.0pt;color:yellow;>a hrefmb.php?urlvariants5.php?create&referenceGenome>Addimg srcimages/tree_expand.png width12px height12px altcreate />/a>/span>/li> li>a hrefmb.php?urlvariants.php/in_gene>Transcript Variants/a>/li> li>a hrefmb.php?urlstatus.php>LSDB Status/a>/li> li>a hrefmb.php?urlindex.php&siteadv>span stylefont-size:10.0pt;color:lightyellow;>Advanced Users/a>/span>/li> !-- li>a hrefdata.php>Data/a>/li> li>/li> li>a hrefmb.php?urlindex.php&siteadv>span stylefont-size:10.0pt;color:lightyellow;>Advanced/a>/span>/li> li>a hrefmb17.php?urlindex.php&siteadv>LSDB 3.0.17 beta test/a> ul> li>a hrefmb17.php?urlgenes.php>Genes View beta /a> /li> li>a hrefmb17.php?urltranscripts.php>Transcripts beta/a>/li> li>a hrefmb17.php?urldiseases.php>Mitochondrial Disease beta /a>span stylefont-size:10.0pt;color:yellow;>a hrefmb17.php?urldiseases.php?create>img srcimages/tree_expand.png width12px height12px altcreate />/a>/span>/li> li>a hrefmb17.php?urlvariants.php>Genomic Variants beta /a>span stylefont-size:10.0pt;color:yellow;>a hrefmb17.php?urlvariants5.php?create&referenceGenome>Addimg srcimages/tree_expand.png width12px height12px altcreate />/a>/span>/li> li>a hrefmb17.php?urlvariants.php/in_gene>Transcript Variants beta/a>/li> li>a hrefmb17.php?urlstatus.php>LSDB Status beta/a>/li> /ul> /li> --> /ul> /li> li>a hrefmitobox.php>Tools/a> ul> li>a hrefquickmitome.php>Quick-Mitome for WES/a>/li> li>a hrefquickmitome.php>span stylefont-size:10.0pt;color:blue;> Quick-Mitome/a>/span>/li> li>a hrefquickmitomereport.php>span stylefont-size:10.0pt;color:blue;> Quick-Mitome Report/a>/span>/li> li>a href>/a>mtDNA Tool:/li> li>a hrefmvtool.php> mvTool/a>/li> !-- li>a hrefmvtool5.php> mvTool_v.5/a>/li> --> li>a hrefphymer.php> Phy-Mer/a>/li> li>a hrefmtoolbox.php> MToolBox/a>/li> li>a hrefmv4phylotree.php> mvTool for Haplogroup/a>/li> li>a hrefmvpatho.php> mvTool with HmtDB/a>/li> li>a hrefhttp://www.mitomap.org/foswiki/bin/view/MITOMASTER/WebHome target_blank> MitoMaster/a>/li> li>a hrefhttps://www.mitomap.org/foswiki/bin/view/MITOMAP/MitoTipInfo target_blank> MitoTIP tRNA Scoring/a>/li> li>a hrefhttp://www.mseq.org target_blank titleMSeq-OpenCGA>MSeq-OpenCGA/a>/li> li>a hrefdata.php>/a>Variant Tool:/li> li>a hrefvariant.php> VariantOneStop/a>/li> !-- li>a hrefexomeanalysisrecord.php> Exome Priori. Result/a>/li> --> li>a hrefHBCR.php> /a>HBCR Exome (Retired)/li> li>a hrefhttps://mitomap.org/polg/>POLG Patho. Server/a>/li> li>a hrefhttp://geex.awsomics.org/ target_blank>Data - Awsomics GeEx/a>/li> li>a hrefexpert.php>Expert Panel/a>/li> li>a hrefpanel.php>/a>Panel Tool:/li> li>a hrefgenepanel.php> Gene Panel Examiner/a>/li> li>a hrefgenepanel_nuclearmitome.php> Transgenomic_NuclearMitome/a>/li> li>a hrefped.php>Pedigree Maker/a>/li> li>a hrefjson2table.php>json2table/a>/li>!-- li>a hrefhttp://mseqdr.org:8099/>pdf2table/a>/li> li>a hrefhttp://genomit.eu/work-packages/ target_blank>img srcimages/GENOMIT-logo_neu_1.png width90 height 20 altGENOMIT is an E-Rare funded network of eight partners in Germany, Austria, Italy, France, and USA />/a>/li> li> MitoGenome Diagram: a hrefimages/Mitochondrial_rCRS_HGNC_300dpi_mseqdr.org.pdf target_blank>pdf/a> a hrefimages/Mitochondrial_rCRS_HGNC_300dpi.png target_blank> .png/a>/li> li>a hrefexomiser.php> Exome Prioritization (retired)/a>/li> li>a hrefexome.php>span stylefont-size:10.0pt;color:color:lightblue;>Mito-QuickExome/a>/span>/li> li>a hrefexomiser2a.php>span stylefont-size:10.0pt;color:lightyellow;>Exome_in_5_minutes/a>/span>/li> --> /ul> /li> li> a hrefphenome.php>Phenome-Disease/a> ul> li>a hrefdiag.php>Disease Portal/a>/li> li>a hrefmondo.php>Disease Portal in Mondo/a>/li> li>a hrefhpo_browser.php?3287;>HPO Ontology Browser/a>/li>!-- li>a hrefclinical/index.php target_blank>Clinical_Portal/a>/li> li>a hrefhttp://mseqdr.org:8080/phenotips/PhenoTips/MSEQDR-CHOP-NAMDC-FULL>Core Symptoms (draft)/a>/li> li>a hrefhpo_namdc_review.php>/a>NAMDC-HPO Mapping (retired)/li> li>a hrefexpert.php>Expert Panel/a>/li>--> li>a hrefleigh.php>Leigh Syndrome Resource/a>/li>li>a hrefclinical/index.php target_blank>span stylefont-size:10.0pt;color:blue;>Clinical_Portal/span>/a>/li> li>a hrefclinical/virtualregistry.php target_blank>span stylefont-size:10.0pt;color:blue;> PMD Virtual Registry/span>/a>/li> /ul> /li> li>a href target_blank>/a>Collaboration ul> li>a hrefhttp://www.genesis-app.com/#/login target_blank titleThe Genesis Project provides a flexible, scalable, and easy to use analytics tool that allows scientists to collaborate and analyze genomics data quickly.>Genesis (GEM.App)/a> li>a hrefhttp://genomit.eu/work-packages/ target_blank titleGENOMIT is an E-Rare funded network of eight partners in Germany, Austria, Italy, France, and USA>img srcimages/GENOMIT-logo_neu_1.png width90 height 20 altGENOMIT is an E-Rare funded network of eight partners in Germany, Austria, Italy, France, and USA />/a>/li> li>a hrefhttps://mseqdr.org/leighmap.php target_blank titleLeigh Map is a novel gene-to-phenotype interaction network which can be used as a diagnostic resource for Leigh syndrome (IEMBASE000422; MIM 256000)>LeighMap/a>/li> li>a hrefexpert.php>Expert Panel/a>/li>li>a hrefzone.php target_blank titleProject-specific wiki, forum discussion, chat room, cloud style large file sharing, task, agenda. Create our private project zone.>Collaboration Zone/a>/li> ul> li> -- a hrefzone.php>Overview/a> /li> li> -- a hrefhttp://mseqdr.org:8088/portal/login>Login/a>/li> li> -- a hrefhttp://mseqdr.org:8088/portal/intranet/Register>Register/a>/li> li> -- a hrefhttp://mseqdr.org:8088/portal/g/:spaces:mseqdr_consortium_general/mseqdr_consortium_general>MSeqDR_General/a>/li> /ul> !-- li>a hrefmb17.php?urlIVA>IVA @ CPM/a>/li> li>a hrefhttp://www.cpmbioinfo.net/src/#home target_blank>IVA @ CPM/a> li>a hrefhttps://www.analysis-grid.net/GEM.app/login/? target_blank>GEM.App/a>, now a hrefhttps://www.genesis-app.com/ target_blank>Genesis/a>/li> li>a hrefexomiser_batch3.php> Exome Priori. Target All/a>/li> --> /ul> /li> li> a hrefsubmission.php>Submission/a> ul> !-- li>a hrefmb.php?sitesub&urlms_experiment_design.php>Full Study: Create/a>/li> li>a hrefmb.php?sitesub&urlms_experiment_design_summary.php>Full Study: Manage/a>/li>li>a hrefsubmitvariant.php>Submit Variant/a>/li> li>a hrefmseq.php>MSeq-OpenCGA/a>/li>--> li>a hrefms_variant_submit_clinvar.php>Submit_Interpret_Variant/a>/li> li>a hrefsubmission.php>Instructions/a>/li> !-- li>a hrefms_variant_submit_clinvar.php>Complete Submit/a>/li> li>......span stylefont-size:10.0pt;color:yellow;>a hrefmb.php?urlvariants5.php?create&referenceGenome>Single Variant LOVD Style/a>/span>/li> li>a hrefmb.php?urlvariants5.php?create&referenceGenome>Single Variant LOVD/a> span stylefont-size:10.0pt;color:yellow;>a hrefms_variant_submit_clinvar.php>ClinVar/a>/span>/li> li>a hrefmb.php?urlphenotips>span stylefont-size:10.0pt;color:lightyellow;>Phenotips/a>/span>/li>https://mseqdr.org/phenotips/--> /ul> /li> !-- li>a hrefmp.php?urlphenotips target_blank titleClick here to visit the embedded MSeqDR Phenotips Server.Or visit its native page at the link below: MSeqDR_PhenoTips (Direct_Link) >MSeqDR PhenoTips/a> ul> li>a hrefhttp://10.112.202.35:8080/phenotips/ target_blank>MSeqDR_PhenoTips (Direct_Link)/a>/li> /ul> /li> --> /ul> /div> div idhead_logos_bar> a hrefhttp://www.chla.org/center-personalized-medicine/ target_blank >img srcimages/chla_logo.gif altCHLA_Logo />/a> !-- a hrefhttp://oculargenomics.meei.harvard.edu/ target_blank>img srcimages/round_ogi_logo.png altMEEI_Logo />/a> --> /div> div idhead_user> span stylefont-size:10pt; color:white>b>Hello! Guest! Please a hrefbblogin.php>Login/a> or a hrefbbregister.php>Register/a>! a hrefindex.php?usermodeclinician titleSwitch to Clinician mode to view tools organized for Clinician usage>Clinician Mode/a>/b>/span> /div> div iddiv_botton>/div>/div> div idhead_logo > a hrefindex.php>img classhead_logo_image srcimages/logo_mseqdr.png altMSeqDR Logo width65px height60px>/a> /div> style> #searchbar_ex { display: none; } .head_search:hover #searchbar_ex2 { display:block; } div#head_search:hover ~ div#searchbar_ex2{ transition: all 0.5s ease 2s; background-color: green;}/style>script>$(document).ready(function() {$(#stickyheader).hide(); // hide LOVD header and logo to save spacevar timeout;$(#companylogo).hide(); // hide phenotips big logo to save space$(#tags2).hover( function() { timeout setTimeout(function(){ // do stuff on hover $(#searchbar_ex).show(); }, 1000); //1 seconds }, // function() { $(#searchbar_ex).hide() } function() { timeout setTimeout(function(){ // do stuff on hover $(#searchbar_ex).hide(); }, 9000); //9 seconds } );});/script> div idhead_search classhead_search> form namesearch idsearch actionportal.php methodGET> !--select namedbsource onchangeOnChange(this.form.dbsource);>--> select namedbsource iddbsource> option valuegenomic>Genomic Search/option> option valueOMIM>Disease: OMIM/option> option valueHPO>Disease: HPO/option> /select> input autocompleteoff listdatalist class idtags2 namename size40 typetext placeholderEnter search term here. Mouse-over for examples. titleInput can be: Ensembl, HGNC gene names, chromosome regions, variants (MSCV, dbSNP IDs or HGVS IDs), ClinVar IDs., Disease and phenotype keywords and IDs. Example: 15.89861818G>A,rs113994099, 1:12031905..12081904, POLG, ENSG00000162572, MT-ND1, RCV000000015.1, Myopathy, MELAS. Single entry only!> input typeimage srcimages/search.png altSearch » /> div idresults>/div> /form> /div> div idsearchbar_ex> Examples Gene: a hrefportal.php?dbsourcegenomic&nameMT-ND1>MT-ND1/a>, a hrefportal.php?dbsourcegenomic&namePOLG>POLG/a>, Region: a hrefportal.php?dbsourcegenomic&nameM:1-1000>M:1-1000/a> Variant: a hrefportal.php?dbsourcegenomic&namem.8993T>G>m.8993T>G/a>, a hrefportal.php?dbsourcegenomic&name1:g.10042757T>C>1:g.10042757T>C/a> a hrefportal.php?dbsourcegenomic&namers3888511>rs3888511/a> a hrefportal.php?dbsourcegenomic&nameMSCV_0000006>MSCV_0000006/a>, ClinVar: a hrefportal.php?dbsourcegenomic&nameRCV000000015>RCV000000015/a>, Disease: a hrefportal.php?dbsourceOMIM&nameLeigh syndrome>Leigh syndrome/a>, Phenotype: a hrefportal.php?dbsourceHPO&nameRetinopathy>Retinopathy/a> /div> div iddiv_botton>/div> /div>table cellpadding5 width99% aligncenter border0 cellspacing10 summaryIntroduction of MSeqDR>tbody> tr> td colspan3 aligncenter > span stylefont-size:14pt; color:darkblue>b>MSeqDR: the Mitochondrial Disease Sequence Data Resource Consortium /b>/span> /td>/tr> tr> td colspan1 valigntop width3% alignleft >/td> td colspan1 valigntop bgcolorlightgrey width70% aligncenter stylebgcolor:lightblue> p>span stylefont-size:11.0pt; color:darkblue>b>A global effort, 100+ mitochondrial disease experts./b>/span> p>span stylefont-size:11.0pt; color:darkblue>b>Securely a hrefsubmission.php> span stylefont-size:12pt; color:darkblue>b>collects/b>/span>/a> and a hrefmb.php?urlindex.php>span stylefont-size:12pt; color:darkblue>b>shares/b>/span>/a> data for a hrefdiag.php>span stylefont-size:12pt; color:darkblue>b>rare diseases/b>/span>/a>, patients and causative a hrefmb.php?urlvariants.php>span stylefont-size:12pt; color:darkblue>b>mutations/b>/span>/a>. p>span stylefont-size:11.0pt; color:darkblue>b>a hrefmitobox.php>span stylefont-size:12pt; color:darkblue>b>Tools/b>/span>/a> designed for mitochondrial diseases and a hrefmvtool.php>mtDNA mutations/a>./b>/span> !-- 20180104 Add action oriented blocks -->!-- Action blocks and Browse blocks p>span stylefont-size:14.0pt; color:blue>b>Choose a Tool to Analyze Your Data:/b>/span>--> table width100% classannotationtable height200px cellpadding5 cellspacing5 alignleft border0 stylebackground-color:lightblue;cellpadding:7px; summary > tbody> tr> td width33% aligncenter border0 colspan4>span stylefont-size:14.0pt;align:center; color:blue>b>Choose a Tool to Analyze Your Data:/b>/span> /td>tr> !-- The table header --> tr> td width33% colspan1 aligncenter valigntop titleSingle feature search: Gene, variant, region, disease, phenotype > span stylefont-size:12pt; color:blue>b>I have single gene, variant, region, disease, phenotype /b>/span> /td> td width33% colspan1 aligncenter bgcolorlightyellow valigntop stylemin-width:190px titleMSeqDR and the community developed tools tailed for mitochondrial diseases and mtDNA studies.> span stylefont-size:12pt; color:blue>b>I have variants or genes /b>/span> /td> td width33% colspan1aligncenter valigntop stylemin-width:190px titleMSeqDR Quick-Mitome for mitochondrial diseases and mtDNA data interpretation> span stylefont-size:12pt; color:blue>b>I have VCF from WES or WGS, and clinical data/b>/span> /td> td width33% colspan1 bgcolorlightyellow aligncenter valigntop stylemin-width:190px titleMSeqDR and the community developed tools tailed for mitochondrial diseases and mtDNA studies.> span stylefont-size:12pt; color:blue>b>I have raw sequence data/b>/span> /td> /tr>!-- The table content --> tr> td width33% colspan1 aligncenter valigntop titleSingle feature search: Gene, variant, region, disease, phenotype > !-- span stylefont-size:12pt; color:blue>b>I have single gene, variant, region, disease, phenotype /b>/span> BR>BR> --> div classfree> form namesearch idsearch actionportal.php methodget> select namedbsource iddbsource > option valuegenomic>Genomic Search/option> option valueOMIM>Disease: OMIM/option> option valueHPO>Disease: HPO/option> /select> input autocompleteoff listdatalist class idtags2 namename size23 stylebackground-color:yellow; placeholderEnter search term. Mouse-over for examples. titleInput can be: Ensembl, HGNC gene names, chromosome regions, variants (MSCV, dbSNP IDs or HGVS IDs), ClinVar IDs., Disease and phenotype keywords and IDs. Example: 15.89861818G>A,rs113994099, 1:12031905..12081904, POLG, ENSG00000162572, MT-ND1, RCV000000015.1, Myopathy, MELAS. Single entry only! typetext> input srcimages/search.png altSearch typeimage> /form> div idsearchbar_ex styledisplay: block;align:left> Gene a hrefportal.php?dbsourcegenomic&nameMT-ND1>MT-ND1/a>, a hrefportal.php?dbsourcegenomic&namePOLG>POLG/a>, br>Variant: a hrefportal.php?dbsourcegenomic&namem.8993T>G>m.8993T>G/a> a hrefportal.php?dbsourcegenomic&name1:g.10042757T>C>1:g.10042757T>C/a> a hrefportal.php?dbsourcegenomic&nameMSCV_0000006>MSCV_0000006/a> a hrefportal.php?dbsourcegenomic&namers3888511>rs3888511/a> , br>ClinVar: a hrefportal.php?dbsourcegenomic&nameRCV000000015>RCV000000015/a>, br>Region: a hrefportal.php?dbsourcegenomic&nameM:1-1000>M:1-1000/a> br>Disease: a hrefportal.php?dbsourceOMIM&nameLeigh syndrome>Leigh syndrome/a>, br>Phenotype: a hrefportal.php?dbsourceHPO&nameRetinopathy>Retinopathy/a> /div> /div> /td> td width33% colspan1 aligncenter bgcolorlightyellow valigntop stylemin-width:190px titleMSeqDR and the community developed tools tailed for mitochondrial diseases and mtDNA studies.> !-- span stylefont-size:12pt; color:blue>b>I have variants or Genes/b>/span> p>/p>BR>BR> --> div idtool2 align left width99% stylecolor: darkblue; padding-left: 5px; padding-right: 3px; padding-top: 6px; padding-bottom: 3px;> span stylefont-size:11pt; color:darkblue>b> li>Variant Annotation: br>a hrefmvtool.php>mvTool (mtDNA)***/a>br>br>a hrefvariant.php>OneStopVariant (mtDNA+ nuc. DNA)/a>/li> /br>li>Haplogroup: a hrefphymer.php>Phy-Mer/a>, a hrefhttp://www.mitomap.org/foswiki/bin/view/MITOMASTER/WebHome target_blank>MitoMaster/a>/li> br>li>Gene Annotation: br>a hrefgenepanel2bed.php>Panel Examiner & Universal ID Mapper/a>/li> /b>/span> /div> /td> td width25% colspan1 aligncenter valigntop stylemin-width:190px titleMSeqDR Quick-Mitome for mitochondrial diseases and mtDNA data interpretation> !-- span stylefont-size:12pt; color:blue>b>I have VCF from WES or WGS, and clinical data/b>/span> BR> --> div idtool2 align left width99% stylecolor: darkblue; padding-left: 5px; padding-right: 3px; padding-top: 6px; padding-bottom: 3px;> span stylefont-size:11pt; color:darkblue>b> li>a hrefquickmitome.php>Quick-Mitome/a> Interpretation with Exomiser and HPO/li> /br>li>a hrefclinical/pa.php>HPO Mapping from Clinical Text/a>/li> /br>li>a hrefdiag.php>Disease Browser/a>, a hrefhpo_browser.php?3287;>HPO Browser/a>/li> /b>/span> /div> /td> td width33% colspan1 bgcolorlightyellow aligncenter valigntop stylemin-width:220px titleMSeqDR and the community developed tools tailed for mitochondrial diseases and mtDNA studies.> !-- span stylefont-size:12pt; color:blue>b>I have raw_sequence_data/b>/span> BR>BR> --> div idtool2 align left width99% stylecolor: darkblue; padding-left: 5px; padding-right: 3px; padding-top: 6px; padding-bottom: 3px;> span stylefont-size:11pt; color:darkblue>b> li>Fastq, Fasta, BAM: br>br>li>Haplogroup: a hrefphymer.php>Phy-Mer/a>, a hrefmtoolbox.php>MToolBox/a>, a hrefhttp://www.mitomap.org/foswiki/bin/view/MITOMASTER/WebHome target_blank>MitoMaster/a>/li> br>li>Variant Calling & Annotation: a hrefmtoolbox.php>MToolBox/a>, a hrefhttp://www.mitomap.org/foswiki/bin/view/MITOMASTER/WebHome target_blank>MitoMaster/a>/li> /li> /b>/span> /div> /td> /tr> tr> td width33% aligncenter border0 colspan4>span stylefont-size:14.0pt;align:center; color:blue>b>Choose a Tool to Browse MSeqDR Data:/b>/span> /td>tr> !-- /tbody>/table> p>span stylefont-size:14.0pt; color:blue>b>Choose a Tool to Browse MSeqDR Data:/b>/span> table width100% classannotationtable height200px cellpadding5 cellspacing5 alignleft border0 stylebackground-color:lightblue;cellpadding:7px; summary > tbody> --> tr> td width33% colspan1 height200px aligncenter valigntop titleBoth submission and mining of data for patients, diseases, and pathogenic variants. > a hrefmb.php?urlindex.php>span stylefont-size:12pt; color:blue>b>LSDB: Mutations & Diseases/b>/span> BR> div classlsdb_a_xxxx> div idlsdb_xxxx align left stylecolor: darkblue; padding-left: 12px; padding-right: 3px; padding-top: 10px; padding-bottom: 3px;> span stylefont-size:11pt; color:darkblue>b> li>a hrefmb.php?urlgenes.php>Genes View /a> span stylefont-size:10.0pt;color:yellow;>a hrefmb.php?urlgenes.php?create>Addimg srcimages/tree_expand.png width10px height10px altcreate />/a>/span>/li> br>li>a hrefmb.php?urldiseases.php>Mitochondrial Disease /a>span stylefont-size:10.0pt;color:yellow;>a hrefmb.php?urldiseases.php?create>Addimg srcimages/tree_expand.png width12px height12px altcreate />/a>/span>/li> br>li>a hrefmb.php?urlvariants.php>Genomic Variants /a>span stylefont-size:10.0pt;color:yellow;>a hrefmb.php?urlvariants5.php?create&referenceGenome>Add/a>/span>/li> br>li>a hrefmb.php?urlstatus.php>LSDB Statistics/a>div idleft_nav alignleft > span stylefont-size:9pt; color:darkblue>b>Diseases: a hrefmb.php?urldiseases.php>284/a>/b>/span>span stylefont-size:12.0pt;color:yellow;>a hrefmb.php?urldiseases.php>img srcimages/tree_expand.png width12px height12px altcreate />/a>/span>, span stylefont-size:9pt; color:darkblue>b>Variants: a hrefmb.php?urlvariants.php>28680/26471/a>/b>/span>span stylefont-size:12.0pt;color:yellow;>a hrefhttps://mseqdr.org/submitvariant.php>img srcimages/tree_expand.png width12px height12px altcreate />/a>/span>, span stylefont-size:9pt; color:darkblue>b>Genes: a hrefmb.php?urlgenes.php>1628/a>/b>, span stylefont-size:9pt; color:darkblue>b>mtDNA Tracks: a hrefgbrowse_bridge.php>22/a>/b>/span>/div>/li> br>li>a hrefmb.php?urlindex.php&siteadv>span stylefont-size:10.0pt;color:lightyellow;>Advanced Users/a>/span>/li> /b>/span> /li> /div> !-- div idlsdb_img_xxxx align center> img srcimages/mseqdr_lsdb3_250x250.png width143px height132px altMSeqDR-LSDB />/a> /div> --> /div> /td> td width33% colspan1 height200px aligncenter valigntop titleMSeqDR and the community developed tools tailed for mitochondrial diseases and mtDNA studies.> a hrefmitobox.php>span stylefont-size:12pt; color:blue>b>Data/b>/span> BR> div classtool_a width100%> div idtool_xxxx align left width99% stylecolor: darkblue; padding-left: 5px; padding-right: 3px; padding-top: 6px; padding-bottom: 3px;> span stylefont-size:11pt; color:darkblue>b> li>a hrefdiag.php>Disease Browser/a> (a hrefdiag.php?6873; target\_blank\>Leigh/a>, a hreflhon.php target\_blank\>LHON/a>, a hrefdiag.php?9119;>CPEO/a>, a hrefdiag.php?7588;>MELAS/a>, a hrefdiag.php?8111;>Myopathy/a> ...) /li> br>li>a hrefhpo_browser.php?3287; target\_blank\>HPO Phenotype Browser/a>/li> br>li>a hrefmv4phylotree.php target\_blank\>Haplogroups: PhyloTree & mvTool/a>/li> br>li>Expression Data: a hrefhttp://geex.awsomics.org/ target_blank>Awsomics GeEx /a>/li> br>li>a hrefhttps://mseqdr.org/clinical/cpmrecord.php?typecpmuid&cpmuidMS01001010 target_blank>Patients & Subjects/a>/li> /b>/span> /div> !-- div idtool_img align center> img srcimages/enlarge_white.png width143px height132px alttoolbox />/a> /div> --> /div> /td> td width25% height200px colspan1 aligncenter valigntop titleShow variants and genes in both mitochondrial and nuclear genomes, hosts custom data tracks from user uploads and collaborators.> a hrefhttps://mseqdr.org/gbrowse_bridge.php>span stylefont-size:12pt; color:blue>b>Visualization/b>/span> !-- img srcimages/gbrowse_m_200x160.png width143px height132px altGBrowse />/a> --> br>br> div idtool2 align left width99% stylecolor: darkblue; padding-left: 5px; padding-right: 3px; padding-top: 6px; padding-bottom: 3px;> span stylefont-size:11pt; color:darkblue>b> li> span classwikiexternallink>a hrefhttps://mseqdr.org/gbrowse_bridge.php>MSeqDR GBrowse (Retired)/a>/span> /li> br>li>span classwikiexternallink> MitoGenome Diagram with both HGNC and classical gene names: a hrefimages/Mitochondrial_rCRS_HGNC_300dpi_mseqdr.org.pdf target_blank>pdf/a> !-- a hrefimages/Mitochondrial_rCRS_HGNC_300dpi.png target_blank>png/a> --> a hrefimages/Mitochondrial_rCRS_HGNC_600dpi.tif.zip target_blank>tiff/a>/span>/li> /b>/span> /div> /td> td width33% colspan1 bgcolorlightyellow aligncenter valigntop stylemin-width:220px titleMSeqDR teams> a hrefzone.php>span stylefont-size:12pt; color:blue>b>Collaboration Teams/b>/span>br>br> div idtool2 align left width99% stylecolor: darkblue; padding-left: 5px; padding-right: 3px; padding-top: 6px; padding-bottom: 3px;> span stylefont-size:11pt; color:darkblue>b> li> span classwikiexternallink>a hrefhttp://mseqdr.org:8088/portal/g/:spaces:mseqdr_mtdna_expert_panel/mseqdr_mtdna_expert_panel relnofollow>MSeqDR mtDNA Expert Panel/a>/span> /li> br>li>span classwikiexternallink>a hrefhttp://mseqdr.org:8088/portal/g/:spaces:u24_for_leigh_disease relnofollow>U24 for Leigh Disease/a>/span>/li> br>li>span classwikiexternallink>a hrefhttp://mseqdr.org:8088/portal/g/:spaces:mseqdr_phenotype_cde relnofollow>MSeqDR Phenotype CDE/a>/span>/li>!-- br>li>span classwikiexternallink>a hrefhttp://mseqdr.org:8088/portal/g/:spaces:mseqdr_consortium_general/mseqdr_consortium_general relnofollow>MSeqDR Consortium General/a>/span>/li> --> br>li>span classwikiexternallink>a hrefhttp://mseqdr.org:8088/portal/g/:spaces:umdf_smab/umdf_smab relnofollow>Scientific and Medical Advisory Board (SMAB) of UMDF/a>/li> /b>/span> /div> /td>/tr>/tbody>/table> !-- div idhead_search classhead_search> br>span stylefont-size:12.0pt;line-height:115%;font-family:;Arial;sans-serif;;color:#2E2E2E>Demo Account for MSeqDR and its Phenotips:/span> span stylefont-size:12.0pt;line-height:115%;font-family:;Arial;sans-serif;color:#2E2E2E>User: a hrefhttp://mseqdr.org/phenotips/XWiki/UMDF15>UMDF15/a> , Password: Mito15/span>/p> form namesearch idsearch actionportal.php methodget> select namedbsource iddbsource > option valuegenomic>Genomic Search/option> option valueOMIM>Disease: OMIM/option> option valueHPO>Disease: HPO/option> /select> input autocompleteoff listdatalist class idtags2 namename size70 STYLEbackground-color:yellow; placeholderEnter search term. Mouse-over for examples. titleInput can be: Ensembl, HGNC gene names, chromosome regions, variants (dbSNP IDs or HGVS IDs), ClinVar IDs., Disease and phenotype keywords and IDs. Example: 15.89861818G>A,rs113994099, 1:12031905..12081904, POLG, ENSG00000162572, MT-ND1, RCV000000015.1, Myopathy, MELAS. Single entry only! typetext> input srcimages/search.png altSearch � typeimage> /form> /div> div idsearchbar_ex styledisplay: block;> Quick Examples: Gene a hrefportal.php?dbsourcegenomic&nameMT-ND1>MT-ND1/a>, a hrefportal.php?dbsourcegenomic&namePOLG>POLG/a>, Region: a hrefportal.php?dbsourcegenomic&nameM:1-1000>M:1-1000/a> Variant: a hrefportal.php?dbsourcegenomic&namem.8993T>G>m.8993T>G/a> a hrefportal.php?dbsourcegenomic&name1:g.10042757T>C>1:g.10042757T>C/a> a hrefportal.php?dbsourcegenomic&namers3888511>rs3888511/a> , ClinVar: a hrefportal.php?dbsourcegenomic&nameRCV000000015>RCV000000015/a>, Disease: a hrefportal.php?dbsourceOMIM&nameLeigh syndrome>Leigh syndrome/a>, Phenotype: a hrefportal.php?dbsourceHPO&nameRetinopathy>Retinopathy/a> /div>--> p>span stylefont-size:11.0pt; color:darkblue>b>MSeqDR Demo Account: User: a hrefhttp://mseqdr.org/phenotips/XWiki/UMDF15>UMDF15/a> , Password: Mito15/b>/span> p> br>span stylefont-size:10.5pt; color:darkblue>b>img srcimages/new.jpg width44px height22px altmseqdr new tool />/a> a hrefexpert.php target_blank>MSeqDr Expert Panel for mitochondrial diseases and pathogenic variants/a>. /span> p> span stylefont-size:10.5pt; color:darkblue>b>img srcimages/new.jpg width44px height22px altmseqdr />/a> a href./clinical/cde.php target_blank>Physician Registry Harmonization with HPO-based CDE from 5 Countries/a> a href./clinical/cdereview.php?grouphpo target_blank>(Summary by HPO term)/a> /span> /span> div classview-content> table classviews-view-grid cols-8> tbody> tr classrow-1 row-first row-last> td classcol-1 col-first> div classviews-field views-field-field-flag-country> div classfield-content>img typeoffoaf:Image srcimages/country/australia.jpg alt width30 height20>/div> /div> div classviews-field views-field-field-country-fp> div classfield-content>Australia/div> /div> /td> td classcol-2> div classviews-field views-field-field-flag-country> div classfield-content>img typeoffoaf:Image srcimages/country/germany.gif alt width30 height20>/div> /div> div classviews-field views-field-field-country-fp> div classfield-content>Germany/div> /div> /td> td classcol-3> div classviews-field views-field-field-flag-country> div classfield-content>img typeoffoaf:Image srcimages/country/italy.gif alt width30 height20>/div> /div> div classviews-field views-field-field-country-fp> div classfield-content>Italy/div> /div> /td> td classcol-4> div classviews-field views-field-field-flag-country> div classfield-content>img typeoffoaf:Image srcimages/country/uk.png alt width30 height20>/div> /div> div classviews-field views-field-field-country-fp> div classfield-content>UK/div> /div> /td> td classcol-5 col-last> div classviews-field views-field-field-flag-country> div classfield-content>img typeoffoaf:Image srcimages/country/usa.png alt width30 height20>/div> /div> div classviews-field views-field-field-country-fp> div classfield-content>USA/div> /div> /td> /tr> /tbody>/table> /div> !-- p>span stylefont-size:10.5pt; color:darkblue>b>a hrefhttp://mseqdr.org/clinical>MSeqDR Clinical Tool Portal - Capture and Utilise Standardized Phenotype Data/a> Using a hrefhttp://mseqdr.org:8080/phenotips/PhenoTips/MSEQDR-CHOP-NAMDC-FULL>Core Symptoms/a>/span> /p> p> span stylefont-size:10.5pt; color:darkblue>b>img srcimages/new.jpg width44px height22px altmseqdr />/a> MitoGenome Diagram with gene names in both HGNC and Classical Mito.: a hrefimages/Mitochondrial_rCRS_HGNC_300dpi_mseqdr.org.pdf target_blank>pdf/a> a hrefimages/Mitochondrial_rCRS_HGNC_300dpi.png target_blank>png/a> a hrefimages/Mitochondrial_rCRS_HGNC_600dpi.tif.zip target_blank>tiff (600dpi)/a> p>p>span stylefont-size:11pt; color:darkblue; background:yellow>strong>MSeqDR Tutorial at UMDF Regional Symposium 2017, St Louis/strong>/font>/span> (a hrefhttps://mseqdr.org/doc/MSeqDR_Brief_Intro_Tutorial_UMDF_St_Louis_20170310.doc target_blank>Word/a>, a hrefhttps://mseqdr.org/doc/MSeqDR_Brief_Intro_Tutorial_UMDF_St_Louis_20170310.pdf target_blank>PDF/a>, a hrefhttps://mseqdr.org/doc/MSeqDR_Brief_Intro_Tutorial_UMDF_St_Louis_20170310.html target_blank>Web page/a>) br>span stylefont-size:11pt; color:darkblue; background:yellow>strong>MSeqDR Tutorial at UMDF Mitochondrial Medicine 2017 Washington DC /strong>/font>/span> ( !-- a hrefhttps://mseqdr.org/UMDF16/MSeqDR_Clinician_Tutorial_UMD_Meeting_20170628_FINAL.doc target_blank>Word/a>, a hrefhttps://mseqdr.org/UMDF16/MSeqDR_Clinician_Tutorial_UMD_Meeting_20170628_FINAL.pdf target_blank>PDF/a>) -->div idwp_post styleposition:relative; top:0px; left:1%; align:left; width:85%; font-size:11pt; >br>li> span stylefont-size:12pt; color:darkblue>b>March 26, 2021 /span>a hrefhttps://mseqdr.org/wp/index.php/2021/03/26/preclinical-study-shows-combination-of-vitamins-supplements-may-benefit-mitochondrial-disease/ target_blank titlePreclinical Study Shows Combination of Vitamins, Supplements May Benefit Mitochondrial Disease >Preclinical Study Shows Combination of Vitamins, Supplements May Benefit Mitochondrial Disease/a>/li> br>li> span stylefont-size:12pt; color:darkblue>b>February 22, 2021 /span>a hrefhttps://mseqdr.org/wp/index.php/2021/02/22/gnomad-shares-mtdna-variant-data-from-56434-whole-genome-samples/ target_blank titlegnoMAD shares mtDNA variant data from 56,434 whole genome samples >gnoMAD shares mtDNA variant data from 56,434 whole genome samples/a>/li> br>li> span stylefont-size:12pt; color:darkblue>b> /span>a hrefhttps://mseqdr.org/wp/index.php/2021/02/22/mvtool-v-6-the-mtdna-variant-reference-based-on-316530-whole-genome-sequences/ target_blank titlemvTool v.6: The mtDNA variant reference based on 316,530 whole genome sequences >mvTool v.6: The mtDNA variant reference based on 316,530 whole genome sequences/a>/li> br>li> span stylefont-size:12pt; color:darkblue>b>January 1, 2021 /span>a hrefhttps://mseqdr.org/wp/index.php/2021/01/01/mseqdr-is-migrated-to-new-web-server-at-chla/ target_blank titleMSeqDR is migrated to a new webserver at CHLA >MSeqDR is migrated to a new webserver at CHLA/a>/li> br>li> span stylefont-size:12pt; color:darkblue>b>October 20, 2020 /span>a hrefhttps://mseqdr.org/wp/index.php/2020/10/20/international-research-team-develops-consensus-variant-classification-guidelines-for-genomic-variants-in-mitochondrial-dna/ target_blank titleInternational Research Team Develops Consensus Variant Classification Guidelines for Genomic Variants in Mitochondrial DNA >International Research Team Develops Consensus Variant Classification Guidelines for Genomic Variants in Mitochondrial DNA/a>/li> br>li> span stylefont-size:12pt; color:darkblue>b>August 24, 2020 /span>a hrefhttps://mseqdr.org/wp/index.php/2020/08/24/mvtool-v-5-new-report-layout-and-added-wgs-mtdna-variant-data-from-200000-healthy-people/ target_blank titlemvTool v.5: New report layout and new mtDNA variant data from 200,000 healthy people >mvTool v.5: New report layout and new mtDNA variant data from 200,000 healthy people/a>/li> br>li> span stylefont-size:12pt; color:darkblue>b>July 2, 2020 /span>a hrefhttps://mseqdr.org/wp/index.php/2020/07/02/recent-publications-from-mseqdr-supported-by-the-umdf-and-nih-grants/ target_blank titleRecent publications from MSeqDR supported by the UMDF and NIH grants >Recent publications from MSeqDR supported by the UMDF and NIH grants/a>/li> br>li> span stylefont-size:12pt; color:darkblue>b> /span>a hrefhttps://mseqdr.org/wp/index.php/2020/07/02/clingen-clinvar-mseqdr-working-groups-expert-panels/ target_blank titleClinGen / ClinVar – MSeqDR Working Groups & Expert Panels >ClinGen / ClinVar – MSeqDR Working Groups & Expert Panels/a>/li> br>li> span stylefont-size:12pt; color:darkblue>b>June 30, 2020 /span>a hrefhttps://mseqdr.org/wp/index.php/2020/06/30/clingen-approved-the-mseqdr-consortium-mtdna-svi-specifications-for-mitochondrial-coding-genes/ target_blank titleClinGen approved the MSeqDR Consortium mitochondrial DNA Sequence Variant Interpretation (SVI) specifications >ClinGen approved the MSeqDR Consortium mitochondrial DNA Sequence Variant Interpretation (SVI) specifications/a>/li> br>li> span stylefont-size:12pt; color:darkblue>b>April 29, 2020 /span>a hrefhttps://mseqdr.org/wp/index.php/2020/04/29/u24-mitochondrial-diseases-expert-panel-worked-on-63-gene-and-leigh-disease-at-clingen/ target_blank titleU24 Mitochondrial Diseases Expert Panel is establishing 63 genes’ Leigh Disease associations at ClinGen >U24 Mitochondrial Diseases Expert Panel is establishing 63 genes’ Leigh Disease associations at ClinGen/a>/li> br>span stylefont-size:10.5pt; color:darkblue>b>br>a hrefhttps://projectreporter.nih.gov/project_info_description.cfm?aid9411950 target_blank>MSeqDR U24 grant (1U24HD093483-01) to perform expert curation for Leigh and Leigh-like syndrome genes and variants/a>/span>/div> div classentity-container >figure classentity-figure>/figure>h3 classentity-info>a classjs-entity-name entity-name hrefhttps://www.linkedin.com/groups/8265287 data-app-link>strong> Join MSeqDR LinkedIn Group/strong>: /a>a hrefhttps://mseqdr.org/linkedin.php>img srchttps://mseqdr.org/images/logo_linkedin.png altcreate width224px height31px>/a>/h3>div classentity-meta> /div>/div>/td> td colspan1 valigntop width3% alignleft > /td> /tr> tr>td colspan3 alignleft>!-- div classoe_share s_share> h3> span classo_default_snippet_text>Share/span> a target_Blank classoe_share_facebook hrefhttps://www.facebook.com/sharer/sharer.php?uhttps://mseqdr.org/> i classfa fa-facebook-square>/i> /a> a target_Blank classoe_share_twitter hrefhttps://twitter.com/intent/tweet?textHomepage%20%7C%20CPM%20Sample%20Portal&urlhttp%3A%2F%2F10.252.133.35%3A8069%2F%23scrollTop%3D0> i classfa fa-twitter>/i> /a> a target_Blank classoe_share_linkedin hrefhttp://www.linkedin.com/shareArticle?minitrue&urlhttps://mseqdr.org/;titleMSeqDR.org%20%7C%20CPM%20Sample%20Portal&> i classfa fa-linkedin>/i> /a> a target_Blank classoe_share_google hrefhttps://plus.google.com/share?urlhttps://mseqdr.org/> i classfa fa-google-plus-square>/i> /a> a hrefmailto:?bodyhttps://mseqdr.org/;subjectMSeqDR.org%20Homepage%20%7C%20CPM%20Sample%20Portal> i classfa fa-envelope-o>/i> /a> /h3> /div> br> -->!-- div classcontent stylemargin-left: 1%; 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