tag:blogger.com,1999:blog-385901762024-03-13T09:10:46.457+08:00GenePipe GenePipe is dedicated to bioinformatics analysis on disease gene finding after SNP (single nucleotide polymorphism) markers are identified through an association study. To identify a good candidate disease-susceptibility gene, four major tasks are usually followed in bioinformatics analysis: sequence retrieval with quality check, candidate gene finding, SNP prioritization, and primer design for assays.Unknownnoreply@blogger.comBlogger75125tag:blogger.com,1999:blog-38590176.post-26107209048134929782021-04-16T14:54:00.005+08:002021-04-18T14:26:28.881+08:00GenePipe is shutting down on May 19th, 2021<p>Thank you for all the support of GenePipe these years. Unfortunately, we have to announce our decision to shut down GenePipe permanently on May 19th, 2021 (GMT+8).</p><span><a name='more'></a></span>
Thank you for everything you have done to support all of us during this time.
<div class="separator" style="clear: both;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhTogM3-VimzGKrBQReLfB5e3GBCWN6kgnqxiGa_TqQMYBF0GwBG4dObQOGuo3GC2tH3a0z1r5o-aim74YJMckaIEdMEADXMoOd7F13GrEU19ZyndgnB8nxvm_4iz9ECKIMDRDSfw/s944/pzresult14.png" style="display: block; padding: 1em 0px; text-align: center;"><img alt="" border="0" data-original-height="944" data-original-width="876" height="600" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhTogM3-VimzGKrBQReLfB5e3GBCWN6kgnqxiGa_TqQMYBF0GwBG4dObQOGuo3GC2tH3a0z1r5o-aim74YJMckaIEdMEADXMoOd7F13GrEU19ZyndgnB8nxvm_4iz9ECKIMDRDSfw/s600/pzresult14.png" /></a></div>
<div class="separator" style="clear: both;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDW2UC8XIz5vIdJ3RKaaihfgxt0zzaIpsrf59qoEnQuIdUy3ggTsPWcyD1waBoAJHxh5HBL0iasf2U86JR2nd9mDMPQGdcnaujo8lLLlLnp1T0H3tsEajdLO624KlbqBMPlwEPWA/s2423/variowatchpreview.png" style="display: block; padding: 1em 0px; text-align: center;"><img alt="" border="0" data-original-height="2423" data-original-width="1016" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDW2UC8XIz5vIdJ3RKaaihfgxt0zzaIpsrf59qoEnQuIdUy3ggTsPWcyD1waBoAJHxh5HBL0iasf2U86JR2nd9mDMPQGdcnaujo8lLLlLnp1T0H3tsEajdLO624KlbqBMPlwEPWA/w269-h640/variowatchpreview.png" width="269" /></a></div>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-91408366235551271762018-03-07T10:38:00.000+08:002018-03-07T10:48:28.939+08:00Downtime Notice<div dir="ltr" style="text-align: left;" trbidi="on">
Due to power system maintenance, GenePipe will be offline from 13:00
March 9 to 15:00 March 12, 2018, GMT+8. We apologize for any
inconvenience it may cause.<br />
<br />
Thank
you in advance for your patience. Please contact us with any questions via <span class="anno"> genepipe@ncgm.sinica.edu.tw</span>. </div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-35736386167440399642017-07-05T14:26:00.001+08:002018-03-07T10:49:34.886+08:00Release Notes (2017/07/03)<div dir="ltr" style="text-align: left;" trbidi="on">
<ol style="text-align: left;">
</ol>
VarioWatch which based on Genome Reference Consortium Human Build 38 are released.</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-62365189391258681392017-03-24T17:33:00.001+08:002017-03-24T17:35:03.953+08:00Release Notes (2017/03/24) <div dir="ltr" style="text-align: left;" trbidi="on">
VarioWatch:<br />
<ul style="text-align: left;">
<li>Fix link of PubMed reference</li>
</ul>
SeqTool:<br />
<ul style="text-align: left;">
<li>Fix reference link of NCBI sequence </li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-44998742286199300142017-02-14T11:17:00.000+08:002017-02-14T11:18:03.524+08:00Downtime Notice<div dir="ltr" style="text-align: left;" trbidi="on">
Due to power system maintenance, GenePipe will be unavailable from <span class="anno">18:00 February 14 to 12:00 February 16, 2017, GMT+8</span>. We apologize for any inconvenience.</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-45263529041401825282015-02-16T10:56:00.001+08:002015-02-16T10:56:52.710+08:00Release Notes (2015/02/16)<div dir="ltr" style="text-align: left;" trbidi="on">
PrimerZ:<br />
<br />
<ul style="text-align: left;">
<li>Add chromosome information of <span class="st">compiled data files (.csv - Format).</span></li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-6080074371622452332015-02-11T11:12:00.002+08:002015-02-11T11:12:39.934+08:00Release Notes (2015/02/11)<div dir="ltr" style="text-align: left;" trbidi="on">
PrimerZ:<br />
<br />
<ul style="text-align: left;">
<li>Fix bug of query by Task ID .</li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-11116169022673019342014-10-22T15:42:00.000+08:002017-01-12T15:50:53.727+08:00Release Notes (2014/10/22)<div dir="ltr" style="text-align: left;" trbidi="on">
<br />
<ul style="text-align: left;">
<li>Genepipe now is based on human genome assembly, NCBI Annotation Release 105.</li>
<li>Update dbSNP version to dbSNP141.</li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-91364444741190279152014-04-28T14:53:00.001+08:002014-04-28T14:53:42.128+08:00Release Notes (2014/04/28)<div dir="ltr" style="text-align: left;" trbidi="on">
QualiSeq:<br />
<ul style="text-align: left;">
<li>Fix bug of download sequence of chromosome X/Y .</li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-67817305116994447562014-04-25T10:52:00.002+08:002014-04-25T10:52:54.305+08:00Release Notes (2014/04/25)<div dir="ltr" style="text-align: left;" trbidi="on">
PrimerZ:<br />
<ul style="text-align: left;">
<li>Add new species: Sheep (Genome assembly Oar_v3.1).</li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-6008031469739976462014-04-03T15:53:00.000+08:002014-04-11T16:38:01.625+08:00Release Notes (2014/04/03)<div dir="ltr" style="text-align: left;" trbidi="on">
Database Update<br />
<ul style="text-align: left;">
<li>Genepipe now is based on human genome assembly, NCBI Annotation Release 104.</li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-51988518411108437862014-03-11T15:50:00.001+08:002014-03-11T15:50:42.609+08:00Release Notes (2014/03/11)<div dir="ltr" style="text-align: left;" trbidi="on">
PrimerZ:<br />
<ol style="text-align: left;">
<li>Update Ensembl database to release 75.</li>
<li>Bug fix. </li>
</ol>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-56604201478557489422013-12-27T17:11:00.000+08:002013-12-27T17:11:14.785+08:00Release Notes (2013/12/27)<div dir="ltr" style="text-align: left;" trbidi="on">
PrimerZ:<br />
<br />
<ol>
<li>Update Ensembl database to release 74.</li>
</ol>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-85849665954094342282013-10-24T15:35:00.001+08:002013-10-24T15:36:15.270+08:00Release Notes (2013/10/24)<div dir="ltr" style="text-align: left;" trbidi="on">
PrimerZ:<br />
<ol style="text-align: left;">
<li>Fix bug for validation of In-Silico PCR.</li>
</ol>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-4501841027821461002013-07-03T11:11:00.000+08:002013-07-03T11:11:21.892+08:00Release Notes (2013/07/03)Variowatch:<br />
<ol>
<li>Fix bug of batch query.</li>
</ol>
PrimerZ:<br />
<ol>
<li>Update Ensembl database to release 72.</li>
</ol>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-25759906539380831312013-05-22T15:55:00.001+08:002013-05-22T15:56:22.375+08:00Release Notes (2013/05/22)PrimerZ:<br />
<ol>
<li>Fix bug of masking delection snp. </li>
</ol>
<span id="nav">Qualiseq:</span><br />
<ol>
<li><span id="nav">Update for retrieving date of Ensembl release 71.</span></li>
</ol>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-89653584653932125672013-01-24T15:08:00.000+08:002013-01-24T15:08:18.350+08:00Release Notes (2013/01/24)<div dir="ltr" style="text-align: left;" trbidi="on">
MegaQuery:<br />
<ol style="text-align: left;">
<li>Add location type, TFBS(Transcription factor binding site) for annotation.</li>
</ol>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-53835205478016644462012-12-26T11:29:00.001+08:002012-12-28T14:49:27.286+08:00Release Notes (2012/12/26)GenePipe:<br />
<ol>
<li>Due to the insufficient manpower to maintain STRP-related data, query by STRP markers is unavailable now. </li>
</ol>
<br />
Primer Z:<br />
<ol>
<li>Update Ensembl Database to V69.</li>
</ol>
<br />
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-21928365272210495532012-12-06T17:49:00.001+08:002012-12-06T17:49:40.343+08:00Release Notes (2012/12/06)<div dir="ltr" style="text-align: left;" trbidi="on">
MegaQuery<br />
<ol style="text-align: left;">
<li>Add position start/end in the annotation file, which query by vcf file format.</li>
<li>Bug fix.</li>
</ol>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-58401144786121302612012-10-15T15:07:00.000+08:002012-10-15T15:07:58.184+08:00 Release Notes (2012/10/15) <div dir="ltr" style="text-align: left;" trbidi="on">
Genepipe<br />
<ol style="text-align: left;">
<li>Update dbSNP version to dbSNP137.</li>
</ol>
<br />
PrimerZ<br />
<ol style="text-align: left;">
<li>Bug fix: Query by gene which contains multiple transcripts presents gene transcript graph correctly.</li>
</ol>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-32600623122969795122012-09-19T10:55:00.000+08:002012-09-19T10:55:59.497+08:00Release Notes (2012/09/18)<div dir="ltr" style="text-align: left;" trbidi="on">
Variowatch<br />
<ol style="text-align: left;">
<li>Bug fix: Retrieve disease-related data of genes now works normally.</li>
</ol>
<br />
PrimerZ<br />
<ol style="text-align: left;">
<li>Due to the insufficient manpower to maintain mouse-related databases, query by gene (NCBI) of mouse species is temporarily unavailable.</li>
</ol>
<br />
QualiSeq<br />
<ol style="text-align: left;">
<li>Query by strp(s) now works normally.</li>
</ol>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-28097106394572402612012-08-10T16:55:00.000+08:002012-08-10T16:57:39.184+08:00Release Notes (2012/08/10)<div dir="ltr" style="text-align: left;" trbidi="on">
Database Update<br />
<ol style="text-align: left;">
<li>Genepipe now is based on human genome assembly, NCBI BUILD 37.3.</li>
<li>Update dbSNP version to dbSNP135.</li>
<li>Update data of <a href="http://www.1000genomes.org/" target="_blank">1000 Genomes Project</a> to October 2011 Integrated Variant Set, version 3.</li>
</ol>
VarioWatch<br />
<ol style="text-align: left;"></ol>
<ol style="text-align: left;">
<li>Due to the insufficient manpower to maintain mouse-related database, service of VisualSNP and FANS are temporarily unavailable. For the annotations of human genomic variants, please use <a href="http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do">VarioWatch</a>.</li>
<li><span style="font-family: Arial, Helvetica;">MegaQuery: </span></li>
</ol>
<ul>
<li>Vcf format of annotation result files now is supported.</li>
<li>Incorporate1000 Genome Project data into variant annotation CSV file. </li>
<li>Improve annotation processing efficiency by parallel and streaming upload/download.</li>
<li>Fix minor bugs.</li>
</ul>
<ol style="text-align: left;">
</ol>
PrimerZ<br />
<ol style="text-align: left;">
<li>Fix bug of In-Silicon PCR validation.</li>
<li>Primer-BLAST in NCBI now works normally.</li>
</ol>
SeqTool<br />
<ol style="text-align: left;">
<li> Increase the maximum number of variants for batch query to 10,000. </li>
</ol>
</div>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-2284098336017794882012-05-24T17:58:00.001+08:002012-05-24T17:58:07.627+08:00Release Notes (2012/05/24)<div dir="ltr" style="text-align: left;" trbidi="on">
VarioWatch<br />
<ol style="text-align: left;">
<li>Add information of disease-associated variant from <a href="http://mirdsnp.ccr.buffalo.edu/">miRdSNP</a>, <a href="http://www.snpedia.com/index.php/SNPedia">SNPedia</a> and <a href="http://www.genome.gov/">National Human Genome Research Institute (NHGRI)</a> genome-wide association study (GWAS) catalog data.</li>
<li>Fix bug: Retrieve reference of genes now works normally.</li>
<li>Fix bug of MegaQuery: Variant located within two genes which have the same gene start now can be annotated appropriate.</li>
</ol>
<br />
PrimerZ<br />
<ol style="text-align: left;">
<li>Add new species: Cod, Coelacanth, Gibbon, Horse, Kangaroo Rat, Lamprey, Panda, Tasmanian Devil and Turkey.</li>
<li>Update Ensembl database to release 66.</li>
</ol>
<br />
QualiSeq<br />
<ol style="text-align: left;">
<li>Update Ensembl sequence to release 67.</li>
<li>Fix bug of query by taskID: Retrieve results using url link of taskID now works correctly.</li>
</ol>
<div style="text-align: left;">
</div>
</div>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-63505040929377072302012-04-16T12:12:00.000+08:002012-04-16T17:10:02.605+08:00Release Notes(2012/04/16)<div dir="ltr" style="text-align: left;" trbidi="on">
Fix bugs of VarioWatch and QualiSeq: query by a batch of variations and gene.</div>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-89675419130142218902012-04-09T18:08:00.001+08:002012-04-12T17:00:21.518+08:00Release Notes (2012/04/09)VCF format (version 4.x) input supported<br /><br />MegaQuery Download now supports the annotation of SNP and small indel in Variant Call Format (VCF) version 4.x, with output in CSV format.Unknownnoreply@blogger.com