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.comBlogger50125tag: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-87252428083412686002017-11-30T16:21:00.000+08:002017-11-30T16:21:34.835+08:00Release Notes(2017/11/30)<div dir="ltr" style="text-align: left;" trbidi="on">
Fix URL to the visualized analysis result provided by VarioWatch</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-57150519321364528812017-11-24T10:40:00.000+08:002017-11-24T10:40:18.382+08:00Release Notes(2017/11/16)<div dir="ltr" style="text-align: left;" trbidi="on">
Database information can be downloaded in VarioWatch - MegaQuery Download (GRCh38) </div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-1115239956512656162017-11-14T00:48:00.000+08:002017-11-14T00:48:18.373+08:00Release Notes(2017/11/10)<div dir="ltr" style="text-align: left;" trbidi="on">
Data of <a href="https://www.pharmgkb.org/">PharmGKB
</a> is now incorporated into MegaQuery</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-71562599525033316252017-09-30T15:40:00.002+08:002017-09-30T15:40:16.848+08:00Release Notes(2017/09/30)<div dir="ltr" style="text-align: left;" trbidi="on">
Fix bug of presenting information of ESE and ESS hexamers pattern</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-74252036603555557892017-09-27T11:41:00.002+08:002017-09-27T11:41:54.497+08:00Release Notes(2017/09/27)<div dir="ltr" style="text-align: left;" trbidi="on">
Database information can be downloaded in VarioWatch - MegaQuery Download (GRCh37)</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-91407469234279951262017-08-02T11:39:00.001+08:002017-08-02T18:25:05.172+08:00Release Notes(2017/08/02)<div dir="ltr" style="text-align: left;" trbidi="on">
<ul style="text-align: left;">
<li>Fixing bug of filtering annotated result by location when variant located transcript structure is uncertain.</li>
<li><span class="st">Adjusting supported filter of different input format.</span></li>
</ul>
</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-82660076481700057952017-01-20T11:02:00.000+08:002017-01-20T11:03:18.265+08:00Release Notes (2017/01/20)<div dir="ltr" style="text-align: left;" trbidi="on">
Exons affected by variants, HGVS name of deletion variants and inframe/frameshift evaluations are supported.</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-44272986709301441292016-10-07T13:20:00.000+08:002016-10-07T13:20:04.575+08:00 Release Notes (2016/10/07) <div dir="ltr" style="text-align: left;" trbidi="on">
VarioWatch:<br />
<ul style="text-align: left;">
<li>Fix:<b><span style="font-weight: normal;"><b> </b>retrieving reference from PubMed.</span></b></li>
</ul>
QualiSeq:<br />
<ul style="text-align: left;">
<li>Qualiseq is offline due to the insufficient manpower to
maintain the latest data.</li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-83007694920632664572016-10-07T13:11:00.005+08:002016-10-07T13:11:50.219+08:00 Release Notes (2016/10/05) <div dir="ltr" style="text-align: left;" trbidi="on">
<ul>
<li>Add phenotype data from COSMIC (v78) to MegaQuery.</li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-90656633963554158392016-10-07T13:07:00.001+08:002016-10-07T13:10:33.145+08:00Release Notes (2016/09/05)<div dir="ltr" style="text-align: left;" trbidi="on">
<ul style="text-align: left;">
<li>Add phenotype data from clinvar to MegaQuery.</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-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-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-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-56576641990789961042012-10-22T12:00:00.000+08:002012-10-22T12:00:09.119+08:00Release Notes (2012/10/22) Variowatch<br />
<ol>
<li>Fix bug: Query by sequence now retrive data of hg19 correctly. </li>
</ol>
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.comtag:blogger.com,1999:blog-38590176.post-47264664191946922472012-02-03T15:38:00.001+08:002012-02-03T16:31:08.418+08:00Release Notes(2012/02/02)Bug fixes: The progress bar shows message of invalid taskID when submitting.<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-60137173605362187222011-12-29T17:57:00.002+08:002011-12-30T16:00:50.897+08:00Release Notes(2011/12/30)Add link of VarioWatch result in the MegaQuery Download file (variation_annoation.csv).Unknownnoreply@blogger.com