ab9e4c7bf0b20c84cae8c0c144e97ac5046f8313 gperez2 Wed Jan 8 08:37:26 2025 -0800 Updated the FAQreleases.html#release13 entry and added a link to assemblySearch.html, refs #32596 diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html index 9c2b67a..7ebf837 100755 --- src/hg/htdocs/FAQ/FAQreleases.html +++ src/hg/htdocs/FAQ/FAQreleases.html @@ -1,678 +1,654 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser FAQ" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Frequently Asked Questions: Assembly Releases and Versions</h1> <h2>Topics</h2> <ul> <li><a href="#release1">List of UCSC genome releases</a></li> <li><a href="#release2">Initial assembly release dates</a></li> <li><a href="#patches">Patch sequences for human and mouse</a></li> <li><a href="#release3">UCSC assemblies</a></li> <li><a href="#release4">Comparison of UCSC and NCBI human assemblies</a></li> -<li><a href="#release13">Looking for a genome assembly not shown in the tree?</a></li> +<li><a href="#release13">Finding a genome assembly</a></li> <li><a href="#release12">Differences between UCSC and NCBI mouse assemblies</a></li> <li><a href="#release5">Accessing older assembly versions</a></li> <li><a href="#release6">Frequency of GenBank data updates</a></li> <li><a href="#release7">Coordinate changes between assemblies</a></li> <li><a href="#release8">Converting positions between assembly versions</a></li> <li><a href="#snpConversion">Converting SNPs between assembly versions</a></li> <ul> <li><a href="#snpConversion">How can I convert SNP annotation coordinates between assembly versions?</a></li> <li><a href="#snpLarge">How can I convert a large set of SNP annotations?</a></li> <li><a href="#snpExtract">How can I extract a list of rsIDs using chrom:start-end or vise versa?</a></li> </ul> <li><a href="#release9">Missing annotation tracks</a></li> <li><a href="#release10">What next with the human genome?</a></li> <li><a href="#release11">Mouse strain used for mouse genome sequence</a></li> </ul> <hr> <p> <a href="index.html">Return to FAQ Table of Contents</a></p> <a name="release1"></a> <h2>List of UCSC genome releases</h2> <h6>How do UCSC's release numbers correspond to those of other organizations, such as NCBI?</h6> <p> The first release of an assembly is given a name using the first three characters of the organism's genus and species classification in the format gggSss#, with subsequent assemblies incrementing the number. Assemblies predating the 2003 introduction of the six-letter naming system were given two-letter names in a similar gs# format and human assemblies are named hg# for human genome.</p> <table border=1> <tr> <th>SPECIES</th> <th>UCSC VERSION</th> <th>RELEASE DATE</th> <th>RELEASE NAME</th> <th>STATUS</th> </tr> <tr><td><strong>MAMMALS</strong></td><td></td><td></td><td></td><td></td></tr> <tr><td>Human</td><td>hs1</td><td>Jan. 2022</td><td>T2T Consortium CHM13v2.0</td><td>Available</td></tr> <tr><td></td><td>hg38</td><td>Dec. 2013</td><td>Genome Reference Consortium GRCh38</td><td>Available</td></tr> <tr><td></td><td>hg19</td><td>Feb. 2009</td><td>Genome Reference Consortium GRCh37</td><td>Available</td></tr> <tr><td></td><td>hg18</td><td>Mar. 2006</td><td>NCBI Build 36.1</td><td>Available</td></tr> <tr><td></td><td>hg17</td><td>May 2004</td><td>NCBI Build 35</td><td>Available</td></tr> <tr><td></td><td>hg16</td><td>Jul. 2003</td><td>NCBI Build 34</td><td>Available</td></tr> <tr><td></td><td>hg15</td><td>Apr. 2003</td><td>NCBI Build 33</td><td>Archived</td></tr> <tr><td></td><td>hg13</td><td>Nov. 2002</td><td>NCBI Build 31</td><td>Archived</td></tr> <tr><td></td><td>hg12</td><td>Jun. 2002</td><td>NCBI Build 30</td><td>Archived</td></tr> <tr><td></td><td>hg11</td><td>Apr. 2002</td><td>NCBI Build 29</td><td>Archived (data only)</td></tr> <tr><td></td><td>hg10</td><td>Dec. 2001</td><td>NCBI Build 28</td><td>Archived (data only)</td></tr> <tr><td></td><td>hg8</td><td>Aug. 2001</td><td>UCSC-assembled</td><td>Archived (data only)</td></tr> <tr><td></td><td>hg7</td><td>Apr. 2001</td><td>UCSC-assembled</td><td>Archived (data only)</td></tr> <tr><td></td><td>hg6</td><td>Dec. 2000</td><td>UCSC-assembled</td><td>Archived (data only)</td></tr> <tr><td></td><td>hg5</td><td>Oct. 2000</td><td>UCSC-assembled</td><td>Archived (data only)</td></tr> <tr><td></td><td>hg4</td><td>Sep. 2000</td><td>UCSC-assembled</td><td>Archived (data only)</td></tr> <tr><td></td><td>hg3</td><td>Jul. 2000</td><td>UCSC-assembled</td><td>Archived (data only)</td></tr> <tr><td></td><td>hg2</td><td>Jun. 2000</td><td>UCSC-assembled</td><td>Archived (data only)</td></tr> <tr><td></td><td>hg1</td><td>May 2000</td><td>UCSC-assembled</td><td>Archived (data only)</td></tr> <tr><td>Alpaca</td><td>vicPac2</td><td>Mar. 2013</td><td>Broad Institute Vicugna_pacos-2.0.1</td><td>Available</td></tr> <tr><td></td><td>vicPac1</td><td>Jul. 2008</td><td>Broad Institute VicPac1.0</td><td>Available</td></tr> <tr><td>Armadillo</td><td>dasNov3</td><td>Dec. 2011</td><td>Broad Institute DasNov3</td><td>Available</td></tr> <tr><td>Baboon</td><td>papAnu4</td><td>Apr. 2017</td><td>Human Genome Sequencing Center</td><td>Available</td></tr> <tr><td></td><td>papAnu2</td><td>Mar. 2012</td><td>Baylor College of Medicine Panu_2.0</td><td>Available</td></tr> <tr><td></td><td>papHam1</td><td>Nov. 2008</td><td>Baylor College of Medicine HGSC Pham_1.0</td><td>Available</td></tr> <tr><td>Bison</td><td>bisBis1</td><td>Oct. 2014</td><td>Univ. of Maryland Bison_UMD1.0</td><td>Available</td></tr> <tr><td>Bonobo</td><td>panPan3</td><td>May 2020</td><td>University of Washington</td><td>Available</td></tr> <tr><td></td><td>panPan2</td><td>Dec. 2015</td><td>Max-Planck Institute for Evolutionary Anthropology panpan1.1</td><td>Available</td></tr> <tr><td></td><td>panPan1</td><td>May 2012</td><td>Max-Planck Institute panpan1</td><td>Available</td></tr> <tr><td>Brown kiwi</td><td>aptMan1</td><td>Jun. 2015</td><td>Max-Planck Institute for Evolutionary Anthropology AptMant0</td><td>Available</td></tr> <tr><td>Bushbaby</td><td>otoGar3</td><td>Mar. 2011</td><td>Broad Institute OtoGar3</td><td>Available</td></tr> <tr><td>Cat</td><td>felCat9</td><td>Nov. 2017</td><td> Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine Felis_catus_9.0</td><td>Available</td></tr> <tr><td></td><td>felCat8</td><td>Nov. 2014</td><td>ICGSC Felis_catus_8.0</td><td>Available</td></tr> <tr><td></td><td>felCat5</td><td>Sep. 2011</td><td>ICGSC Felis_catus-6.2</td><td>Available</td></tr> <tr><td></td><td>felCat4</td><td>Dec. 2008</td><td>NHGRI catChrV17e</td><td>Available</td></tr> <tr><td></td><td>felCat3</td><td>Mar. 2006</td><td>Broad Institute Release 3</td><td>Available</td></tr> <tr><td>Chimp</td><td>panTro6</td><td>Jan. 2018</td><td>Clint_PTRv2</td><td>Available</td></tr> <tr><td></td><td>panTro5</td><td>May 2016</td><td>CGSC Build 3.0</td><td>Available</td></tr> <tr><td></td><td>panTro4</td><td>Feb. 2011</td><td>CGSC Build 2.1.4</td><td>Available</td></tr> <tr><td></td><td>panTro3</td><td>Oct. 2010</td><td>CGSC Build 2.1.3</td><td>Available</td></tr> <tr><td></td><td>panTro2</td><td>Mar. 2006</td><td>CGSC Build 2.1</td><td>Available</td></tr> <tr><td></td><td>panTro1</td><td>Nov. 2003</td><td>CGSC Build 1.1</td><td>Available</td></tr> <tr><td>Chinese hamster</td><td>criGri1</td><td>Jul. 2013</td><td>Beijing Genomics Institution-Shenzhen C_griseus_v1.0</td><td>Available</td></tr> <tr><td>Chinese hamster ovary cell line</td><td>criGriChoV2</td><td>Jun. 2017</td><td>Eagle Genomics Ltd CHOK1S_HZDv1</td><td>Available</td></tr> <tr><td></td><td>criGriChoV1</td><td>Aug. 2011</td><td>Beijing Genomics Institute CriGri_1.0</td><td>Available</td></tr> <tr><td>Chinese pangolin</td><td>manPen1</td><td>Aug. 2014</td><td>Washington University (WashU) M_pentadactyla-1.1.1</td><td>Available</td></tr> <tr><td>Cow</td><td>bosTau9</td><td>Apr. 2018</td><td>USDA ARS</td><td>Available</td></tr> <tr><td></td><td>bosTau8</td><td>Jun. 2014</td><td>University of Maryland v3.1.1</td><td>Available</td></tr> <tr><td></td><td>bosTau7</td><td>Oct. 2011</td><td>Baylor College of Medicine HGSC Btau_4.6.1</td><td>Available</td<tr> <tr><td></td><td>bosTau6</td><td>Nov. 2009</td><td>University of Maryland v3.1</td><td>Available</td></tr> <tr><td></td><td>bosTau4</td><td>Oct. 2007</td><td>Baylor College of Medicine HGSC Btau_4.0</td><td>Available</td></tr> <tr><td></td><td>bosTau3</td><td>Aug. 2006</td><td>Baylor College of Medicine HGSC Btau_3.1</td><td>Available</td></tr> <tr><td></td><td>bosTau2</td><td>Mar. 2005</td><td>Baylor College of Medicine HGSC Btau_2.0</td><td>Available</td></tr> <tr><td></td><td>bosTau1</td><td>Sep. 2004</td><td>Baylor College of Medicine HGSC Btau_1.0</td><td>Archived</td></tr> <tr><td>Crab-eating macaque</td><td>macFas5</td><td>Jun. 2013</td><td>Washington University Macaca_fascicularis_5.0</td><td>Available</td></tr> <tr><td>Dog</td><td>canFam6</td><td>Oct. 2020</td><td>Dog Genome Sequencing Consortium Dog10K_Boxer_Tasha</td><td>Available</td></tr> <tr><td></td><td>canFam5</td><td>May 2019</td><td>University of Michigan</td><td>Available</td></tr> <tr><td></td><td>canFam4</td><td>Mar. 2020</td><td>Uppsala University</td><td>Available</td></tr> <tr><td></td><td>canFam3</td><td>Sep. 2011</td><td>Broad Institute v3.1</td><td>Available</td></tr> <tr><td></td><td>canFam2</td><td>May 2005</td><td>Broad Institute v2.0</td><td>Available</td></tr> <tr><td></td><td>canFam1</td><td>Jul. 2004</td><td>Broad Institute v1.0</td><td>Available</td></tr> <tr><td>Dolphin</td><td>turTru2</td><td>Oct. 2011</td><td>Baylor College of Medicine Ttru_1.4</td><td>Available</td></tr> <tr><td>Elephant</td><td>loxAfr3</td><td>Jul. 2009</td><td>Broad Institute LoxAfr3</td><td>Available</td></tr> <tr><td>Ferret</td><td>musFur1</td><td>Apr. 2011</td><td>Ferret Genome Sequencing Consortium MusPutFur1.0</td><td>Available</td></tr> <tr><td>Garter snake</td><td>thaSir1</td><td>Jun. 2015</td><td>Washington University Thamnophis_sirtalis-6.0</td><td>Available</td></tr> <tr><td>Gibbon</td><td>nomLeu3</td><td>Oct. 2012</td><td>Gibbon Genome Sequencing Consortium Nleu3.0</td><td>Available</td></tr> <tr><td></td><td>nomLeu2</td><td>Jun. 2011</td><td>Gibbon Genome Sequencing Consortium Nleu1.1</td><td>Available</td></tr> <tr><td></td><td>nomLeu1</td><td>Jan. 2010</td><td>Gibbon Genome Sequencing Consortium Nleu1.0</td><td>Available</td></tr> <tr><td>Golden eagle</td><td>aquChr2</td><td>Oct. 2014</td><td>University of Washington aquChr2-1.0.2</td><td>Available</td></tr> <tr><td>Golden snub-nosed monkey</td><td>rhiRox1</td><td>Oct. 2014</td><td>Novogene Rrox_v1</td><td>Available</td></tr> <tr><td>Gorilla</td><td>gorGor6</td><td>Aug. 2019</td><td>University of Washington</td><td>Available</td></tr> <tr><td></td><td>gorGor5</td><td>Mar. 2016</td><td>University of Washington GSMRT3</td><td>Available</td></tr> <tr><td></td><td>gorGor4</td><td>Dec. 2014</td><td>Wellcome Trust Sanger Institute gorGor4</td><td>Available</td></tr> <tr><td></td><td>gorGor3</td><td>May 2011</td><td>Wellcome Trust Sanger Institute gorGor3.1</td><td>Available</td></tr> <tr><td>Green Monkey</td><td>chlSab2</td><td>Mar. 2014</td><td>Vervet Genomics Consortium 1.1</td><td>Available</td></tr> <tr><td>Guinea pig</td><td>cavPor3</td><td>Feb. 2008</td><td>Broad Institute cavPor3</td><td>Available</td></tr> <tr><td>Hawaiian monk seal</td><td>neoSch1</td><td>Jun. 2017</td><td>Johns Hopkins University ASM220157v1</td><td>Available</td></tr> <tr><td>Hedgehog</td><td>eriEur2</td><td>May 2012</td><td>Broad Institute EriEur2.0</td><td>Available</td></tr> <tr><td></td><td>eriEur1</td><td>Jun. 2006</td><td>Broad Institute Draft_v1</td><td>Available</td></tr> <tr><td>Horse</td><td>equCab3</td><td>Jan. 2018</td><td>University of Louisville</td><td>Available</td></tr> <tr><td></td><td>equCab2</td><td>Sep. 2007</td><td>Broad Institute EquCab2</td><td>Available</td></tr> <tr><td></td><td>equCab1</td><td>Jan. 2007</td><td>Broad Institute EquCab1</td><td>Available</td></tr> <tr><td>Kangaroo rat</td><td>dipOrd1</td><td>Jul. 2008</td><td>Baylor/Broad Institute DipOrd1.0</td><td>Available</td></tr> <tr><td>Little brown bat</td><td>myoLuc2</td><td>Jul. 2010</td><td>Broad Institute MyoLuc2.0</td><td>Available</td></tr> <tr><td>Malayan flying lemur</td><td>galVar1</td><td>Jul. 2014</td><td>WashU G_variegatus-3.0.2</td><td>Available</td></tr> <tr><td>Manatee</td><td>triMan1</td><td>Oct. 2011</td><td>Broad Institute TriManLat1.0</td><td>Available</td></tr> <tr><td>Marmoset</td><td>calJac4</td><td>May 2020</td><td>Washington University Callithrix_jacchus_cj1700_1.1</td><td>Available</td></tr> <tr><td>Marmoset</td><td>calJac3</td><td>Mar. 2009</td><td>WUSTL Callithrix_jacchus-v3.2</td><td>Available</td></tr> <tr><td></td><td>calJac1</td><td>Jun. 2007</td><td>WUSTL Callithrix_jacchus-v2.0.2</td><td>Available</td></tr> <tr><td>Megabat</td><td>pteVam1</td><td>Jul. 2008</td><td>Broad Institute Ptevap1.0</td><td>Available</td></tr> <tr><td>Minke whale</td><td>balAcu1</td><td>Oct. 2013</td><td>KORDI BalAcu1.0</td><td>Available</td></tr> <tr><td>Mouse</td><td>mm39</td><td>Jun. 2020</td><td>Genome Reference Consortium Mouse Build 39</td><td>Available</td></tr> <tr><td></td><td>mm10</td><td>Dec. 2011</td><td>Genome Reference Consortium GRCm38</td><td>Available</td></tr> <tr><td></td><td>mm9</td><td>Jul. 2007</td><td>NCBI Build 37</td><td>Available</td></tr> <tr><td></td><td>mm8</td><td>Feb. 2006</td><td>NCBI Build 36</td><td>Available</td></tr> <tr><td></td><td>mm7</td><td>Aug. 2005</td><td>NCBI Build 35</td><td>Available</td></tr> <tr><td></td><td>mm6</td><td>Mar. 2005</td><td>NCBI Build 34</td><td>Archived</td></tr> <tr><td></td><td>mm5</td><td>May 2004</td><td>NCBI Build 33</td><td>Archived</td></tr> <tr><td></td><td>mm4</td><td>Oct. 2003</td><td>NCBI Build 32</td><td>Archived</td></tr> <tr><td></td><td>mm3</td><td>Feb. 2003</td><td>NCBI Build 30</td><td>Archived</td></tr> <tr><td></td><td>mm2</td><td>Feb. 2002</td><td>MGSCv3</td><td>Archived</td></tr> <tr><td></td><td>mm1</td><td>Nov. 2001</td><td>MGSCv2</td><td>Archived (data only)</td></tr> <tr><td>Mouse lemur</td><td>micMur2</td><td>May 2015</td><td>Baylor/Broad Institute Mmur_2.0</td><td>Available</td></tr> <tr><td></td><td>micMur1</td><td>Jul. 2007</td><td>Broad Institute MicMur1.0</td><td>Available</td></tr> <tr><td>Naked mole-rat</td><td>hetGla2</td><td>Jan. 2012</td><td>Broad Institute HetGla_female_1.0</td><td>Available</td></tr> <tr><td></td><td>hetGla1</td><td>Jul. 2011</td><td>Beijing Genomics Institute HetGla_1.0</td><td>Available</td></tr> <tr><td>Opossum</td><td>monDom5</td><td>Oct. 2006</td><td>Broad Institute release MonDom5</td><td>Available</td></tr> <tr><td></td><td>monDom4</td><td>Jan. 2006</td><td>Broad Institute release MonDom4</td><td>Available</td></tr> <tr><td></td><td>monDom1</td><td>Oct. 2004</td><td>Broad Institute release MonDom1</td><td>Available</td></tr> <tr><td>Orangutan</td><td>ponAbe2</td><td>Jul. 2007</td><td>WUSTL Pongo_albelii-2.0.2</td><td>Available</td></tr> <tr><td></td><td>ponAbe3</td><td>Jan. 2018</td><td>Susie_PABv2/ponAbe3</td><td>Available</td></tr> <tr><td>Panda</td><td>ailMel1</td><td>Dec. 2009</td><td>BGI-Shenzhen AilMel 1.0</td><td>Available</td></tr> <tr><td>Pig</td><td>susScr11</td><td>Feb. 2017</td><td>Swine Genome Sequencing Consortium Sscrofa11.1</td><td>Available</td></tr> <tr><td></td><td>susScr3</td><td>Aug. 2011</td><td>Swine Genome Sequencing Consortium Sscrofa10.2</td><td>Available</td></tr> <tr><td></td><td>susScr2</td><td>Nov. 2009</td><td>Swine Genome Sequencing Consortium Sscrofa9.2</td><td>Available</td></tr> <tr><td>Pika</td><td>ochPri3</td><td>May 2012</td><td>Broad Institute OchPri3.0</td><td>Available</td></tr> <tr><td></td><td>ochPri2</td><td>Jul. 2008</td><td>Broad Institute OchPri2</td><td>Available</td></tr> <tr><td>Platypus</td><td>ornAna2</td><td>Feb. 2007</td><td>WUSTL v5.0.1</td><td>Available</td></tr> <tr><td></td><td>ornAna1</td><td>Mar. 2007</td><td>WUSTL v5.0.1</td><td>Available</td></tr> <tr><td>Proboscis Monkey</td><td>nasLar1</td><td>Nov. 2014</td><td>Proboscis Monkey Functional Genome Consortium Charlie1.0</td><td>Available</td></tr> <tr><td>Rabbit</td><td>oryCun2</td><td>Apr. 2009</td><td>Broad Institute release OryCun2</td><td>Available</td></tr> <tr><td>Rat</td><td>rn7</td><td>Nov. 2020</td><td>Wellcome Sanger Institute mRatBN7.2</td><td>Available</td></tr> <tr><td></td><td>rn6</td><td>Jul. 2014</td><td>RGSC Rnor_6.0</td><td>Available</td></tr> <tr><td></td><td>rn5</td><td>Mar. 2012</td><td>RGSC Rnor_5.0</td><td>Available</td></tr> <tr><td></td><td>rn4</td><td>Nov. 2004</td><td>Baylor College of Medicine HGSC v3.4</td><td>Available</td></tr> <tr><td></td><td>rn3</td><td>Jun. 2003</td><td>Baylor College of Medicine HGSC v3.1</td><td>Available</td></tr> <tr><td></td><td>rn2</td><td>Jan. 2003</td><td>Baylor College of Medicine HGSC v2.1</td><td>Archived</td></tr> <tr><td></td><td>rn1</td><td>Nov. 2002</td><td>Baylor College of Medicine HGSC v1.0</td><td>Archived</td></tr> <tr><td>Rhesus</td><td>rheMac10</td><td>Feb. 2019</td><td>The Genome Institute at Washington University School of Medicine Mmul_10</td><td>Available</td></tr> <tr><td></td><td>rheMac8</td><td>Nov. 2015</td><td>Baylor College of Medicine HGSC Mmul_8.0.1</td><td>Available</td></tr> <tr><td></td><td>rheMac3</td><td>Oct. 2010</td><td>Beijing Genomics Institute CR_1.0</td><td>Available</td></tr> <tr><td></td><td>rheMac2</td><td>Jan. 2006</td><td>Baylor College of Medicine HGSC v1.0 Mmul_051212</td><td>Available</td></tr> <tr><td></td><td>rheMac1</td><td>Jan. 2005</td><td>Baylor College of Medicine HGSC Mmul_0.1</td><td>Archived</td></tr> <tr><td>Rock hyrax</td><td>proCap1</td><td>Jul. 2008</td><td>Baylor College of Medicine HGSC Procap1.0</td><td>Available</td></tr> <tr><td>Sheep</td><td>oviAri4</td><td>Dec. 2015</td><td>ISGC Oar_v4.0</td><td>Available</td></tr> <tr><td></td><td>oviAri3</td><td>Aug. 2012</td><td>ISGC Oar_v3.1</td><td>Available</td></tr> <tr><td></td><td>oviAri1</td><td>Feb. 2010</td><td>ISGC Ovis aries 1.0</td><td>Available</td></tr> <tr><td>Shrew</td><td>sorAra2</td><td>Aug. 2008</td><td>Broad Institute SorAra2.0</td><td>Available</td></tr> <tr><td></td><td>sorAra1</td><td>Jun. 2006</td><td>Broad Institute SorAra1.0</td><td>Available</td></tr> <tr><td>Sloth</td><td>choHof1</td><td>Jul. 2008</td><td>Broad Institute ChoHof1.0</td><td>Available</td></tr> <tr><td>Squirrel</td><td>speTri2</td><td>Nov. 2011</td><td>Broad Institute SpeTri2.0</td><td>Available</td></tr> <tr><td>Squirrel monkey</td><td>saiBol1</td><td>Oct. 2011</td><td>Broad Institute SaiBol1.0</td><td>Available</td></tr> <tr><td>Tarsier</td><td>tarSyr2</td><td>Sep. 2013</td><td>WashU Tarsius_syrichta-2.0.1</td><td>Available</td></tr> <tr><td></td><td>tarSyr1</td><td>Aug. 2008</td><td>WUSTL/Broad Institute Tarsyr1.0</td><td>Available</td></tr> <tr><td>Tasmanian devil</td><td>sarHar1</td><td>Feb. 2011</td><td>Wellcome Trust Sanger Institute Devil_refv7.0</td><td>Available</td></tr> <tr><td>Tenrec</td><td>echTel2</td><td>Nov. 2012</td><td>Broad Institute EchTel2.0</td><td>Available</td></tr> <tr><td></td><td>echTel1</td><td>Jul. 2005</td><td>Broad Institute echTel1</td><td>Available</td></tr> <tr><td>Tree shrew</td><td>tupBel1</td><td>Dec. 2006</td><td>Broad Institute Tupbel1.0</td><td>Available</td></tr> <tr><td>Wallaby</td><td>macEug2</td><td>Sep. 2009</td><td>Tammar Wallaby Genome Sequencing Consortium Meug_1.1</td><td>Available</td></tr> <tr><td>White rhinoceros</td><td>cerSim1</td><td>May 2012</td><td>Broad Institute CerSimSim1.0</td><td>Available</td></tr> <tr><td><strong></strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><strong>VERTEBRATES</strong></td><td></td><td></td><td></td><td></td></tr> <tr><td>African clawed frog</td><td>xenLae2</td><td>Aug. 2016</td><td>Int. Xenopus Sequencing Consortium</td><td>Available</td></tr> <tr><td>American alligator</td><td>allMis1</td><td>Aug. 2012</td><td>Int. Crocodilian Genomes Working Group allMis0.2</td><td>Available</td></tr> <tr><td>Atlantic cod</td><td>gadMor1</td><td>May 2010</td><td>Genofisk GadMor_May2010</td><td>Available</td></tr> <tr><td>Budgerigar</td><td>melUnd1</td><td>Sep. 2011</td><td>WUSTL v6.3</td><td>Available</td></tr> <tr><td>Chicken</td><td>galGal6</td><td>Mar. 2018</td><td>GRCg6 Gallus-gallus-6.0</td><td>Available</td></tr> <tr><td></td><td>galGal5</td><td>Dec. 2015</td><td>ICGC Gallus-gallus-5.0</td><td>Available</td></tr> <tr><td></td><td>galGal4</td><td>Nov. 2011</td><td>ICGC Gallus-gallus-4.0</td><td>Available</td></tr> <tr><td></td><td>galGal3</td><td>May 2006</td><td>WUSTL Gallus-gallus-2.1</td><td>Available</td></tr> <tr><td></td><td>galGal2</td><td>Feb. 2004</td><td>WUSTL Gallus-gallus-1.0</td><td>Available</td></tr> <tr><td>Coelacanth</td><td>latCha1</td><td>Aug. 2011</td><td>Broad Institute LatCha1</td><td>Available</td></tr> <tr><td>Elephant shark</td><td>calMil1</td><td>Dec. 2013</td><td>IMCB Callorhinchus_milli_6.1.3</td><td>Available</td></tr> <tr><td>Fugu</td><td>fr3</td><td>Oct. 2011</td><td>JGI v5.0</td><td>Available</td></tr> <tr><td></td><td>fr2</td><td>Oct. 2004</td><td>JGI v4.0</td><td>Available</td></tr> <tr><td></td><td>fr1</td><td>Aug. 2002</td><td>JGI v3.0</td><td>Available</td></tr> <tr><td>Lamprey</td><td>petMar3</td><td>Dec. 2017</td><td>University of Kentucky Pmar_germline 1.0</td><td>Available</td></tr> <tr><td></td><td>petMar2</td><td>Sep. 2010</td><td>WUGSC 7.0</td><td>Available</td></tr> <tr><td></td><td>petMar1</td><td>Mar. 2007</td><td>WUSTL v3.0</td><td>Available</td></tr> <tr><td>Lizard</td><td>anoCar2</td><td>May 2010</td><td>Broad Institute AnoCar2</td><td>Available</td></tr> <tr><td></td><td>anoCar1</td><td>Feb. 2007</td><td>Broad Institute AnoCar1</td><td>Available</td></tr> <tr><td>Medaka</td><td>oryLat2</td><td>Oct. 2005</td><td>NIG v1.0</td><td>Available</td></tr> <tr><td>Medium ground finch</td><td>geoFor1</td><td>Apr. 2012</td><td>BGI GeoFor_1.0 / NCBI 13302</td><td>Available</td></tr> <tr><td>Nile tilapia</td><td>oreNil2</td><td>Jan. 2011</td><td>Broad Institute Release OreNil1.1</td><td>Available</td></tr> <tr><td>Painted turtle</td><td>chrPic1</td><td>Dec. 2011</td><td>IPTGSC Chrysemys_picta_bellii-3.0.1</td><td>Available</td></tr> <tr><td>Stickleback</td><td>gasAcu1</td><td>Feb. 2006</td><td>Broad Institute Release 1.0</td><td>Available</td></tr> <tr><td>Tetraodon</td><td>tetNig2</td><td>Mar. 2007</td><td>Genoscope v7</td><td>Available</td></tr> <tr><td></td><td>tetNig1</td><td>Feb. 2004</td><td>Genoscope v7</td><td>Available</td></tr> <tr><td>Tibetan frog</td><td>nanPar1</td><td>Mar. 2015</td><td>Beijing Genomics Institute BGI_ZX_20015</td><td>Available</td></tr> <tr><td>Turkey</td><td>melGal5</td><td>Nov. 2014</td><td>Turkey Genome Consortium v5.0</td><td>Available</td></tr> <tr><td></td><td>melGal1</td><td>Dec. 2009</td><td>Turkey Genome Consortium v2.01</td><td>Available</td></tr> <tr><td><em>X. tropicalis</em></td><td>xenTro10</td><td>Nov. 2019</td><td>University of California, Berkeley UCB_Xtro_10.0</td><td>Available</td></tr> <tr><td></td><td>xenTro9</td><td>Jul. 2016</td><td>JGI v.9.1</td><td>Available</td></tr> <tr><td></td><td>xenTro7</td><td>Sep. 2012</td><td>JGI v.7.0</td><td>Available</td></tr> <tr><td></td><td>xenTro3</td><td>Nov. 2009</td><td>JGI v.4.2</td><td>Available</td></tr> <tr><td></td><td>xenTro2</td><td>Aug. 2005</td><td>JGI v.4.1</td><td>Available</td></tr> <tr><td></td><td>xenTro1</td><td>Oct. 2004</td><td>JGI v.3.0</td><td>Available</td></tr> <tr><td>Zebra finch</td><td>taeGut2</td><td>Feb. 2013</td><td>WashU taeGut324</td><td>Available</td></tr> <tr><td></td><td>taeGut1</td><td>Jul. 2008</td><td>WUSTL v3.2.4</td><td>Available</td></tr> <tr><td>Zebrafish</td><td>danRer11</td><td>May 2017</td><td>Genome Reference Consortium GRCz11 </td><td>Available</td></tr> <tr><td></td><td>danRer10</td><td>Sep. 2014</td><td>Genome Reference Consortium GRCz10 </td><td>Available</td></tr> <tr><td></td><td>danRer7</td><td>Jul. 2010</td><td>Sanger Institute Zv9 </td><td>Available</td></tr> <tr><td></td><td>danRer6</td><td>Dec. 2008</td><td>Sanger Institute Zv8 </td><td>Available</td></tr> <tr><td></td><td>danRer5</td><td>Jul. 2007</td><td>Sanger Institute Zv7 </td><td>Available</td></tr> <tr><td></td><td>danRer4</td><td>Mar. 2006</td><td>Sanger Institute Zv6 </td><td>Available</td></tr> <tr><td></td><td>danRer3</td><td>May 2005</td><td>Sanger Institute Zv5 </td><td>Available</td></tr> <tr><td></td><td>danRer2</td><td>Jun. 2004</td><td>Sanger Institute Zv4 </td><td>Archived</td></tr> <tr><td></td><td>danRer1</td><td>Nov. 2003</td><td>Sanger Institute Zv3 </td><td>Archived</td></tr> <tr><td><strong></strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><strong>DEUTEROSTOMES</strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><em>C. intestinalis</em></td><td>ci3</td><td>Apr. 2011</td><td>Kyoto KH</td><td>Available</td></tr> <tr><td><em>C. intestinalis</em></td><td>ci2</td><td>Mar. 2005</td><td>JGI v2.0</td><td>Available</td></tr> <tr><td><em></em></td><td>ci1</td><td>Dec. 2002</td><td>JGI v1.0</td><td>Available</td></tr> <tr><td>Lancelet</td><td>braFlo1</td><td>Mar. 2006</td><td>JGI v1.0</td><td>Available</td></tr> <tr><td><em>S. purpuratus</em></td><td>strPur2</td><td>Sep. 2006</td><td>Baylor College of Medicine HGSC v. Spur 2.1</td><td>Available</td></tr> <tr><td></td><td>strPur1</td><td>Apr. 2005</td><td>Baylor College of Medicine HGSC v. Spur_0.5</td><td>Available</td></tr> <tr><td><strong></strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><strong>INSECTS</strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><em>A. mellifera</em></td><td>apiMel2</td><td>Jan. 2005</td><td>Baylor College of Medicine HGSC v.Amel_2.0 </td><td>Available</td></tr> <tr><td><em></em></td><td>apiMel1</td><td>Jul. 2004</td><td>Baylor College of Medicine HGSC v.Amel_1.2 </td><td>Available</td></tr> <tr><td><em>A. gambiae</em></td><td>anoGam3</td><td>Oct. 2006</td><td>International Consortium for the Sequencing of Anopheles Genome AgamP3</td><td>Available</td></tr> <tr><td><em></em></td><td>anoGam1</td><td>Feb. 2003</td><td>IAGP v.MOZ2</td><td>Available</td></tr> <tr><td><em>D. ananassae</em></td><td>droAna2</td><td>Aug. 2005</td><td>Agencourt Arachne release</td><td>Available</td></tr> <tr><td></td><td>droAna1</td><td>Jul. 2004</td><td>TIGR Celera release</td><td>Available</td></tr> <tr><td><em>D. erecta</em></td><td>droEre1</td><td>Aug. 2005</td><td>Agencourt Arachne release</td><td>Available</td></tr> <tr><td><em>D. grimshawi</em></td><td>droGri1</td><td>Aug. 2005</td><td>Agencourt Arachne release</td><td>Available</td></tr> <tr><td><em>D. melanogaster</em></td><td>dm6</td><td>Aug. 2014</td><td>BDGP Release 6 + ISO1 MT</td><td>Available</td></tr> <tr><td><em></em></td><td>dm3</td><td>Apr. 2006</td><td>BDGP Release 5</td><td>Available</td></tr> <tr><td><em></em></td><td>dm2</td><td>Apr. 2004</td><td>BDGP Release 4</td><td>Available</td></tr> <tr><td></td><td>dm1</td><td>Jan. 2003</td><td>BDGP Release 3</td><td>Available</td></tr> <tr><td><em>D. mojavensis</em></td><td>droMoj2</td><td>Aug. 2005</td><td>Agencourt Arachne release</td><td>Available</td></tr> <tr><td></td><td>droMoj1</td><td>Aug. 2004</td><td>Agencourt Arachne release</td><td>Available</td></tr> <tr><td><em>D. persimilis</em></td><td>droPer1</td><td>Oct. 2005</td><td>Broad Institute release</td><td>Available</td></tr> <tr><td><em>D. pseudoobscura</em></td><td>dp3</td><td>Nov. 2004</td><td>FlyBase Release 1.0</td><td>Available</td></tr> <tr><td><em></em></td><td>dp2</td><td>Aug. 2003</td><td>Baylor College of Medicine HGSC Freeze 1</td><td>Available</td></tr> <tr><td><em>D. sechellia</em></td><td>droSec1</td><td>Oct. 2005</td><td>Broad Institute Release 1.0</td><td>Available</td></tr> <tr><td><em>D. simulans</em></td><td>droSim1</td><td>Apr. 2005</td><td>WUSTL Release 1.0</td><td>Available</td></tr> <tr><td><em>D. virilis</em></td><td>droVir2</td><td>Aug. 2005</td><td>Agencourt Arachne release</td><td>Available</td></tr> <tr><td></td><td>droVir1</td><td>Jul. 2004</td><td>Agencourt Arachne release</td><td>Available</td></tr> <tr><td><em>D. yakuba</em></td><td>droYak2</td><td>Nov. 2005</td><td>WUSTL Release 2.0</td><td>Available</td></tr> <tr><td></td><td>droYak1</td><td>Apr. 2004</td><td>WUSTL Release 1.0</td><td>Available</td></tr> <tr><td><strong></strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><strong>NEMATODES</strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><em>C. brenneri</em></td><td>caePb2</td><td>Feb. 2008</td><td>WUSTL 6.0.1</td><td>Available</td></tr> <tr><td><em></em></td><td>caePb1</td><td>Jan. 2007</td><td>WUSTL 4.0</td><td>Available</td></tr> <tr><td><em>C. briggsae</em></td><td>cb3</td><td>Jan. 2007</td><td>WUSTL Cb3</td><td>Available</td></tr> <tr><td><em></em></td><td>cb1</td><td>Jul. 2002</td><td>WormBase v. cb25.agp8</td><td>Available</td></tr> <tr><td><em>C. elegans</em></td><td>ce11</td><td>Feb. 2013</td><td>C. elegans Sequencing Consortium WBcel235</td><td>Available</td></tr> <tr><td></td><td>ce10</td><td>Oct. 2010</td><td>WormBase v. WS220</td><td>Available</td></tr> <tr><td></td><td>ce6</td><td>May 2008</td><td>WormBase v. WS190</td><td>Available</td></tr> <tr><td></td><td>ce4</td><td>Jan. 2007</td><td>WormBase v. WS170</td><td>Available</td></tr> <tr><td></td><td>ce2</td><td>Mar. 2004</td><td>WormBase v. WS120</td><td>Available</td></tr> <tr><td></td><td>ce1</td><td>May 2003</td><td>WormBase v. WS100</td><td>Archived</td></tr> <tr><td><em>C. japonica</em></td><td>caeJap1</td><td>Mar. 2008</td><td>WUSTL 3.0.2</td><td>Available</td></tr> <tr><td><em>C. remanei</em></td><td>caeRem3</td><td>May 2007</td><td>WUSTL 15.0.1</td><td>Available</td></tr> <tr><td><em></em></td><td>caeRem2</td><td>Mar. 2006</td><td>WUSTL 1.0</td><td>Available</td></tr> <tr><td><em>P. pacificus</em></td><td>priPac1</td><td>Feb. 2007</td><td>WUSTL 5.0</td><td>Available</td></tr> <tr><td><strong></strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><strong>OTHER</strong></td><td></td><td></td><td></td><td></td></tr> <tr><td>Sea Hare</td><td>aplCal1</td><td>Sep. 2008</td><td>Broad Release Aplcal2.0</td><td>Available</td></tr> <tr><td>Yeast</td><td>sacCer3</td><td>April 2011</td><td>SGD April 2011 sequence</td><td>Available</td></tr> <tr><td></td><td>sacCer2</td><td>June 2008</td><td>SGD June 2008 sequence</td><td>Available</td></tr> <tr><td></td><td>sacCer1</td><td>Oct. 2003</td><td>SGD 1 Oct 2003 sequence</td><td>Available</td></tr> <tr><td><strong></strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><strong>VIRUSES</strong></td><td></td><td></td><td></td><td></td></tr> <tr><td>Ebola Virus</td><td>eboVir3</td><td>June 2014</td><td>Sierra Leone 2014 (G3683/KM034562.1)</td><td>Available</td></tr> <tr><td>Monkeypox Virus</td><td>mpxvRivers</td><td>May 2022</td><td>MPXV-M5312_HM12_Rivers (MT903340.1/GCF_014621545.1)</td><td>Available</td></tr> <tr><td>SARS-CoV-2</td><td>wuhCor1</td><td>Jan. 2020</td><td>SARS-CoV-2 ASM985889v3</td><td>Available</td></tr> </table> <a name="release2"></a> <h2>Initial assembly release dates</h2> <h6>When will the next assembly be out?</h6> <p> UCSC does not produce its own genome assemblies, but instead obtains them from standard sources. Because of this, you can expect us to release a new version of a genome soon after the assembling organization has released the version. A new assembly release initially consists of the genome sequence and a small set of aligned annotation tracks. Additional annotation tracks are added as they are obtained or generated. Bulk downloads of the data are typically available in the first week after the assembly is released in the browser.</p> <a name="patches"></a> <h2>Patch sequences for genome assemblies</h2> <h6>Why am I seeing chr_alt or chr_fix chromosomes on the Genome Browser?</h6> <p> Since the intial <a href="https://www.ncbi.nlm.nih.gov/grc" target="_blank">Genome Reference Consortium</a> (GRC) release of the human and mouse genome assemblies, there have been updates to these assemblies known as "patches". Patches are accessioned scaffold sequences that add information to the assembly without disrupting the chromosome coordinates. Patches are given chromosome context by aligning the sequence to the current assembly. Together the scaffod sequence and the alignment define the patch to the genome assembly. The GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they can introduce duplication. </p> <p> There are two kinds of GRC patch sequences, <a href="/FAQ/FAQdownloads#downloadAlt" target="_blank">chr_alt</a> and <a href="/FAQ/FAQdownloads#downloadFix" target="_blank">chr_fix</a> sequences: </p> <ul> <li><b>Novel patches (alternative haplotypes)</b> - Chromosomal regions of the genome that exhibit sufficient variability to prevent adequate representation by a single sequence. Also referred to as alternate loci. The Genome Browser labels these haplotype sequences by appending "<em>_alt</em>" to their names, i.e., <em>chr5_KI270794v1_alt</em>.</li> <li><b>Fix patches</b> - Error corrections (addressed by approaches such as base changes, component replacements/updates, switch-point updates or tiling-path changes) or assembly improvements, such as the extension of sequence into gaps. The Genome Browser labels these fix sequences by appending "<em>_fix</em>" to their names, i.e., <em>chr1_KN538361v1_fix</em>.</li> </ul> <p> The <a href="https://genome-blog.gi.ucsc.edu/blog/2019/02/22/patches/" target="_blank">Patching up the Genome</a> blog post contains more information on how patch sequences are incorporated into the UCSC Genome Browser. For more information about how patch sequences can affects BLAT and isPCR results, please refer to the following <a href="/FAQ/FAQblat.html#blat1c" target="_blank">BLAT FAQ</a>.</p> <a name="release3"></a> <h2>Data sources - UCSC assemblies</h2> <h6>Where does UCSC obtain the assembly and annotation data displayed in the Genome Browser?</h6> <p> All the assembly data displayed in the UCSC Genome Browser are obtained from external sequencing centers. To determine the data source and version for a given assembly, see the assembly's description on the Genome Browser <a href="../cgi-bin/hgGateway">Gateway</a> page or the <a href="#release1">List of UCSC Genome Releases</a>.</p> <p> The annotations accompanying an assembly are obtained from a variety of sources. The UCSC Genome Bioinformatics Group generates several of the tracks; the remainder are contributed by collaborators at other sites. Each track has an associated description page that credits the authors of the annotation.</p> <p> For detailed information about the individuals and organizations who contributed to a specific assembly, see the <a href="../goldenPath/credits.html">Credits</a> page.</p> <a name="asmEquivalent"></a> <h6>Which UCSC assemblies are equivalent to Ensembl or NCBI assemblies?</h6> <p> The asmEquivalent table on the hgFixed database is available on the public MySQL server to show which assemblies versions are identical (or almost identical) to each other between UCSC, Ensembl, Genbank, and RefSeq assemblies.</p> <pre> mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -e 'desc asmEquivalent;' hgFixed +----------------------+-------------------------------------------+ | Field | Type | +----------------------+-------------------------------------------+ | source | varchar(255) | | destination | varchar(255) | | sourceAuthority | enum('ensembl','ucsc','genbank','refseq') | | destinationAuthority | enum('ensembl','ucsc','genbank','refseq') | | matchCount | bigint(20) | | sourceCount | bigint(20) | | destinationCount | bigint(20) | +----------------------+-------------------------------------------+</pre> <p> The "Count" indications are the count of individual sequences in the assembly. When all three counts are identical, <code>matchCount == sourceCount == destinationCount</code>, then the match between genome assemblies is perfectly identical.</p> <p> Non-perfect matches can be due to a number of factors: <ol> <li>different or not included chrMT genome sequences in an assembly</li> <li>identical duplicated sequences present or absent from an assembly</li> <li>some smaller contigs not included in an assembly</li> <li>slight differences in versions of assemblies where some contain sequences not in the other assembly</li> </ol> </p> <a name="release4"></a> <h2>Comparison of UCSC and NCBI human assemblies</h2> <h6>How do the human assemblies displayed in the UCSC Genome Browser differ from the NCBI human assemblies?</h6> <p> Human assemblies displayed in the Genome Browser (hg10 and higher) are near identical to the NCBI assemblies when it comes to primary sequence. Minor differences may be present, however. Sources include:</p> <ul> <li>NCBI genomes are repeat masked with RepeatMasker, however, UCSC genomes are independently masked with both RepeatMasker (with different flags) and WindowMasker, ultimately using the program output with the highest percentage masked for the base sequence</li> <li>In genome download files, UCSC uses the 'chr1' nomenclature for sequence identifiers, whereas the primary NCBI sequence identifiers are RefSeq accessions</li> <li>The original mitochondrion (chrM) for hg19 differs from the one in NCBI (GRCh37)</li> <li>The mitochondrion released by NCBI after the hg19 browser was built has been added to the assemby as chrMT. See our <a href = "FAQgenes.html#mito" target = _blank>documentation</a> for details.</li> </ul> -<h2 id=release13>Looking for a genome assembly not shown in the tree?</h2> -<p> -When looking for a specific assembly, the best place to start is the <a -href="/cgi-bin/hgGateway">Gateway page</a>. If you begin to type the common name, species name, or -NCBI RefSeq accession number in the search box on the left side of the screen, -suggestions will appear if any matches are found. -This search will also match any <a href="/goldenPath/help/hgTrackHubHelp.html#Assembly"> -assembly hubs</a> that are listed in UCSC's -<a href="/cgi-bin/hgHubConnect">Public Hubs</a>. Nearly every NCBI RefSeq assembly -and Vertebrate Genomes Project assembly is included here within the -<a href="../goldenPath/newsarch.html#060121">GenArk hubs</a>. -NCBI RefSeq assemblies can be loaded with direct links such as -<a href="http://genome.ucsc.edu/h/GCF_001984765.1"> -http://genome.ucsc.edu/h/GCF_001984765.1</a> with the <b>GCF</b> accession. -These assembly hubs are automatically updated, but not reviewed by UCSC. -The species tree shows all genomes reviewed by UCSC.</p> - +<h2 id=release13>Finding a genome assembly</h2> <p> -If the assembly of interest is not found, please visit our -<a href="/assemblyRequest.html">assembly request page</a>. -Search that page for your assembly. If there is a "view" -link you can launch the existing genome browser. Otherwise, -click the "request" button to fill out a form to -add your genome of interest. An existing <b>GCA_</b> or <b>GCF_</b> -identifier must exist, reflecting that the assembly has been deposited -into Genbank at NCBI, before we can process it. See the <a target="_blank" -href="https://www.ncbi.nlm.nih.gov/assembly/docs/submission/"> -Assembly Submission Guidelines page</a> at NCBI for directions on -their submission process if your genome needs to be deposited. -Also, review the <a target="_blank" href="https://bit.ly/UCSC_blog_GenArk"</a>UCSC GenArk Blog posts</a> -for examples of accessing and reviewing technical details about GenArk hubs.</p> - +If the assembly of interest is not listed on the <a href="/cgi-bin/hgGateway">Gateway page</a>, +visit the <a href="/assemblySearch.html">Genome assembly search and request page</a>. Search for the +assembly, and if no "view" link exists, click "request" to submit a form. A +GCA_ or GCF_ identifier is required, indicating the assembly is deposited in GenBank at NCBI. For +additional details, refer to +<a target="_blank" href="https://www.ncbi.nlm.nih.gov/assembly/docs/submission/"> +NCBI's Assembly Submission Guidelines</a> and the +<a target="_blank" href="https://bit.ly/UCSC_blog_GenArk"</a>UCSC GenArk Blog</a>.</p> <p> Another option available to all users is to create an <a href="/goldenPath/help/hgTrackHubHelp.html#Assembly"> assembly hub</a>. These are assemblies created and hosted by users and displayed on the Genome Browser. This requires no intervention by the UCSC Genome Browser and can be done for any assembly. See our <a href="/goldenPath/help/hubQuickStartAssembly.html"> Quick Start Guide to Assembly Hubs page</a> for additional information and resources. If you create an assembly hub, consider sharing it with others as a -<a href="/cgi-bin/hgHubConnect">Public Hub</a>.</p> - -<p> -If you would like information about creating a track hub for an existing assembly hub, please refer -to the following <a href="/FAQ/FAQlink.html#trackHubLoading">FAQ entry</a>.</p> +<a href="/cgi-bin/hgHubConnect">Public Hub</a>. If you would like information about creating a +track hub for an existing assembly hub, please refer to the following +<a href="/FAQ/FAQlink.html#trackHubLoading">FAQ entry</a>.</p> <a name="release12"></a> <h2>Differences between UCSC and NCBI mouse assemblies</h2> <h6>Is the mouse genome assembly displayed in the UCSC Genome Browser the same as the one on the NCBI website?</h6> <p> The mouse genome assemblies featured in the UCSC Genome Browser are the same as those on the NCBI web site with one difference: the UCSC versions contain only the reference strain data (C57BL/6J). NCBI provides data for several additional strains in their builds.</p> <a name="release5"></a> <h2>Accessing older assembly versions</h2> <h6>I need to access an older version of a genome assembly that's no longer listed in the Genome Browser menu. What should I do?</h6> <p> In addition to the assembly versions currently available in the Genome Browser, you can access the data for older assemblies of the browser through our <a href="http://hgdownload.soe.ucsc.edu/downloads.html" target="_blank">Downloads</a> page.</p> <a name="release6"></a> <h2>Frequency of GenBank data updates</h2> <h6>How frequently does UCSC update its databases with new data from GenBank?</h6> <p> GenBank updates for mRNA, RefSeq, and EST data occur on a semi-quarterly basis, following major NCBI releases. These updates are in place for most Genome Browser assemblies. Assemblies that are not on an incremental update schedule are updated whenever we load a new assembly or make a major revision to a table.</p> <p> <a name="release7"></a> <h2>Coordinate changes between assemblies </h2> <h6>I noticed that the chromosomal coordinates for a particular gene that I'm looking at have changed since the last time I used your browser. What happened?</h6> <p> A common source of confusion for users arises from mixing up different assemblies. It is very important to be aware of which assembly you are looking at. Within the Genome Browser display, assemblies are labeled by organism and date. To look up the corresponding UCSC database name or NCBI build number, use the <a href="#release1">release table</a>.</p> <p> UCSC database labels are of the form hg<em>#</em>, panTro<em>#</em>, etc. The letters designate the organism, e.g. <em>hg</em> for human genome or <em>panTro</em> for <em>Pan troglodytes</em>. The number denotes the UCSC assembly version for that organism. For example, ce1 refers to the first UCSC assembly of the <em>C. elegans</em> genome.</p> <p> The coordinates of your favorite gene in one assembly may not be the same as those in the next release of the assembly unless the gene happens to lie on a completely sequenced and unrevised chromosome. For information on integrating data from one assembly into another, see the <a href="#release8">Converting positions between assembly versions</a> section.</p> <a name="release8"></a> <h2>Converting positions between assembly versions</h2> <h6>I've been researching a specific area of the human genome on the current assembly, and now you've just released a new version. Is there an easy way to locate my area of interest on the new assembly?</h6> <p> See the section on <a href="FAQdownloads.html#download28">converting coordinates</a> for information on assembly migration tools.</p> <a name="snpConversion"></a> <h2>Converting SNPs between assembly versions</h2> <h6>How can I convert SNP annotation coordinates between assembly versions?</h6> <p> While the LiftOver tool exists to convert coordinates between assemblies, <b>it is NOT recommended to use LiftOver</b> to convert SNPs between two assembly versions. Using LiftOver to convert a very small region, especially a single base SNP, is not always a trivial task as the alignment may not get a high enough score to be considered a successful conversion.</p> <p> The mapping from one genome assembly to the next is automatically generated from sequence alignments and is not complete nor perfect, just a best attempt. The stability of rsIDs is why we recommend mapping across assemblies using rsIDs first and then falling back to using cross-assembly mappings to look up the positions of items that didn't map. When an rsID in hg18 is not found in the hg38 dbSNP data, that rsID has been withdrawn or replaced by a different rsID. In that case, mapping the hg18 position of the disappeared rsID to hg38 and looking for a new rsID at the corresponding position may help to find the new rsID.</p> <p> dbSNP started assigning rsIDs in the 1990s, before the human genome was assembled. At that point, SNPs were defined by flanking sequences with the varying base(s) in the middle -- local sequence context, with no genomic location because there was no genome. rsIDs are supposed to be stable across genome assemblies despite the changing genomic positions. Regardless of the genome assembly version, "rs429358" refers to the same polymorphic variant in the 4th exon of the ApoE gene with T as the major allele and C as the minor allele. Its genomic position in hg18 is chr19:50103781, and its genomic position in hg38 is chr19:44908684.</p> <p> <b>Instead, the recommended process</b> to convert a SNP's coordinates between assemblies is to use a SNP track to search for each rsID on the target genome assembly. For example, after creating a list of rsIDs for your conversion, you would then search for each rsID on the target's Genome Browser using the dbSNP track for human assemblies (i.e. hg19 or hg38) or the EVA SNP track on mouse assemblies (i.e. mm10 or mm39) to perform the conversion.</p> <p>To summarize the setps:</p> <ol> <li>Create a file of all rsIDs</li> <li>Use the Table Browser to map the file of rsIDs to the other assembly's coordinates</li> <li>Create another file containing any rsIDs that were not mapped by the Table Browser</li> <li>Using the file from the previous step, use the Table Browser to create a BED4 file for the rsIDs that were not mapped by the Table Browser</li> <li>Run LiftOver on the BED4 file to get the new coordinates in the other assembly</li> <li>Use the Data Integrator to map the LiftOver results to new rsIDs where possible</li> <li>Combine the Table Browser rsID-mapped BED4 with the LiftOver/Data Integrator-mapped BED4. Beware duplicates that will cause downstream problems. You will need to decide whether to remove duplicates as unreliable or resolve duplicates</li> </ol> <a name="snpLarge"></a> <h6>How can I convert a large set of SNP annotations?</h6> <p> For bulk conversions, the <a href="/cgi-bin/hgTables">Table Browser</a> can be used to extract the coordinates for the rsIDs on the target assembly. More information about performing batch queries on the Table Browser can be found on the following <a href="/goldenPath/help/hgTablesHelp.html#BatchQuery">Table Browser help page</a>. An example of using the Table Browser to convert SNP between assemblies can be found on a previously answered question available on the <a href="https://groups.google.com/a/soe.ucsc.edu/g/genome/c/SM0Ae7NMf4k/m/oh4_M8DeAgAJ" target="_blank">mailing list archive</a>. </p> <p> If you are using versions dbSNP 153 and above, the data are formatted as bigBed files instead of being stored as a MariaDb table. For very large queries, this may cause the Table Browser to timeout before the query finishes as dbSNP has grown to include over 700 million variants. If you find that your Table Browser query timesout for your list of rsIDs, you can use the <code>bigBedNamedItems</code> command-line tool to extract the rsID coordinates directly from the bigBed file instead of using the Table Browser.</p> <p>More information and examples using the <code>bigBedNamedItems</code> utility can be found on the following <a href="FAQdownloads.html#snp">FAQ entry</a>. As a reminder, you can run any Kent command-line tool without arguments to get the usage statement. </p> <a name="snpExtract"></a> <h6>How can I extract a list of rsIDs using chrom:start-end or vice versa?</h6> <p> Several utilities for working with bigBed-formatted binary files can be downloaded <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. Run a utility with no arguments to see a brief description of the utility and its options. </p> <ul> <li><b>bigBedInfo</b> provides summary statistics about a bigBed file including the number of items in the file. With the <b>-as</b> option, the output includes an autoSql definition of data columns, useful for interpreting the column values.</li> <li><b>bigBedToBed</b> converts the binary bigBed data to tab-separated text. Output can be restricted to a particular region by using the -chrom, -start and -end options. </li> <li><b>bigBedNamedItems</b> extracts rows for one or more rs# IDs.</li> </ul> <a name="snpExamples"></a> <h6>Examples:</h6> <ol> <li>Retrieve all variants in the region chr1:200001-200400 <pre><tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp155.bb -chrom=chr1 -start=200000 -end=200400 stdout</tt></pre> </li> <li>Retrieve variant rs6657048 <pre><tt>bigBedNamedItems dbSnp155.bb rs6657048 stdout</tt></pre> </li> <li>Retrieve all variants with rs# IDs in a file (myIds.txt) and output to another file (dbSnp155.myIds.bed) <pre><tt>bigBedNamedItems -nameFile dbSnp155.bb myIds.txt dbSnp155.myIds.bed</tt></pre> </li> </ol> <a name="release9"></a> <h2>Missing annotation tracks</h2> <h6>Why is my favorite annotation track missing from your latest release?</h6> <p> The initial release of a new genome assembly typically contains a small subset of core annotation tracks. New tracks are added as they are generated. In many cases, our annotation tracks are contributed by scientists not affiliated with UCSC who must first obtain the sequence, repeatmasked data, etc. before they can produce their tracks. If you have need of an annotation that has not appeared on an assembly within a month or so of its release, feel free to send an inquiry to <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. <!-- above address is genome at soe.ucsc.edu --> <strong><em><span class="gbsWarnText">Messages sent to this address will be posted to the moderated genome mailing list, which is archived on a SEARCHABLE, PUBLIC <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">Google Groups forum</a></span></em></strong>. </p> <a name="release10"></a> <h2>What next with the human genome?</h2> <h6>Now that the human genome is "finished", will there be any more releases?</h6> <p> Rest assured that work will continue. There will be updates to the assembly over the next several years. This has been the case for all other finished (i.e. essentially complete) genome assemblies as gaps are closed. For example, the <em>C. elegans</em> genome has been "finished" for several years, but small bits of sequence are still being added and corrections are being made. NCBI will continue to coordinate the human genome assemblies in collaboration with the individual chromosome coordinators, and UCSC will continue to QC the assembly in conjunction with NCBI (and, to a lesser extent, Ensembl). UCSC, NCBI, Ensembl, and others will display the new releases on their sites as they become available.</p> <a name="release11"></a> <h2>Mouse strain used for mouse genome sequence</h2> <h6>What strain of mouse was used for the Mus musculus genome?</h6> <p> C57BL/6J.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->