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.comBlogger51125tag: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-58182995090341267882017-08-22T23:46:00.001+08:002017-08-22T23:46:57.174+08:00Release Notes(2017/08/22)<div dir="ltr" style="text-align: left;" trbidi="on">
<ul style="text-align: left;">
<li>Fix link of NCBI Primer-BLAST and
Primer3</li>
<li>Fix bug of masking SNP with large deletion</li>
</ul>
</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-33943367374263747972017-07-28T11:47:00.000+08:002017-07-28T11:47:05.746+08:00Release Notes(2017/07/28)<div dir="ltr" style="text-align: left;" trbidi="on">
<br />
Fix bug of primer design for genes on the reverse strand with snp masked.</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-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-67105114767574227972013-03-06T13:09:00.000+08:002013-03-06T13:10:05.823+08:00Release Notes (2013/03/06)Primer Z:<br />
<ol>
<li>Update Ensembl Database to release 70.</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-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-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-53485588591520140722011-08-11T10:58:00.001+08:002011-08-11T11:03:35.042+08:00Release Notes(2011/08/08)<ol><li>QualiSeq: update Ensembl human genome sequence to release 63.</li><li>PrimerZ: update Ensembl database to release 63.</li><li>Variowatch bug fix: motif sequence of ESE and ESS mapping to target sequence on reverse strand displayed incorrectly from 3 prime end to 5 prime end.</li><li>New function of Variowatch: fast download of annotations for millions of variants.</li></ol>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-67950143952588825272011-06-24T09:59:00.002+08:002011-06-24T10:00:03.192+08:00Release Notes(2011/06/23)1.VarioWatch has been updated to human genome NCBI Build 37.2<br />
2.Update database of PrimerZ to NCBI Build 37.2Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-3681232017652244682011-04-26T16:57:00.004+08:002011-04-27T09:53:18.717+08:00Release Notes (2011/04/26)<ol><li>VarioWatch has been updated to a beta version based on human genome NCBI Build 37.1</li><li>Update database of PrimerZ to Ensembl Release 62 and NCBI Build 37.1<br /></li><li>Fix SeqTool SNP extraction problem with older dbSNP version (131).</li></ol>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-4319680841084504912011-03-08T17:30:00.001+08:002011-04-26T17:04:51.330+08:00Release Notes (2011/03/08)1. Update human genome sequence from Ensembl to release 61 of the QualiSeq.<br />2. Update database of PrimerZ to Ensembl Release 61.<br />3. Upgrade human genome assembly version to NCBI 37.2 and dbSNP to version 132 of VisualSNP<br />4. Upgrade human genome assembly version to NCBI 37.2 and fix the analysis of mouse variats query of FANSUnknownnoreply@blogger.comtag:blogger.com,1999:blog-38590176.post-55790361341179761602010-09-06T17:25:00.001+08:002010-09-06T17:26:11.968+08:00Release Notes(2010/09/06)1.Update Ensembl data to v59.<br />
2.Update Journal Reference.<br />
3.Fix Fans, VisualSNP and QualiSeq bug.<br />
4.Update Hapmap data (Allele frequencies 2010/08_phaseII+III)<br />
5.Fix PrimerZ config file <br />
<br />Unknownnoreply@blogger.com