d1f7caa72759548b36c87954a6b19f700658d7ae ccpowell Mon Jul 29 15:45:10 2019 -0700 Adding equCab3 to FAQrelease, refs #21223 diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html index 1625e50..8d9df7e 100755 --- src/hg/htdocs/FAQ/FAQreleases.html +++ src/hg/htdocs/FAQ/FAQreleases.html @@ -1,518 +1,519 @@ <!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="#release3">UCSC assemblies</a></li> <li><a href="#release4">Comparison of UCSC and NCBI human assemblies</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="#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> <li><a href="#release13">UniProt (Swiss-Prot/TrEMBL) display changes</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>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>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>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>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>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>equCab2</td><td>Sep. 2007</td><td>Broad Institute EquCab2</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>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>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>Microbat</td><td>myoLuc2</td><td>Jul. 2010</td><td>Broad Institute MyoLuc2.0</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>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>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>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>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> </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="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="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> Recent human assemblies displayed in the Genome Browser (hg10 and higher) are identical to the NCBI assemblies.</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> Daily and weekly incremental updates of mRNA, RefSeq, and EST data are in place for several of the more recent 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> Data are updated on the following schedule:</p> <ul> <li> Native and xeno mRNA and refSeq tracks: updated daily for human and mouse assemblies; updated approximately weekly for all other organisms</li> <li> EST data: updated weekly on Saturday morning</li> <li> Downloadable data files: updated weekly on Saturday morning</li> <li> Outdated sequences - removed once per quarter</li> </ul> <p> Mirror sites are not required to use an incremental update process, and should not experience problems as a result of these updates.</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="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> <a name="release13"></a> <h2>UniProt (Swiss-Prot/TrEMBL) display changes</h2> <h6>What has UCSC done to accommodate the changes to display IDs recently introduced by UniProt (aka Swiss-Prot/TrEMBL)?</h6> <p> Here is a detailed description of the database changes we have made to accommodate the UniProt changes. If you are using the <em>proteinID</em> field in our knownGene table or the Swiss-Prot/TrEMBL display ID for indexing or cross-referencing other data, we strongly suggest you transition to the UniProt accession number. These changes will also affect anyone who is mirroring our site.</p> <ol> <li> The latest UniProt Knowledgebase (Release 46.0, Feb. 1st, 2005) was parsed and the results were stored in a newly created database <em>sp050201</em>.</li> <li> A corresponding database, <em>proteins050201</em>, was constructed based on data in <em>sp050201</em> and other protein data sources.</li> <li> Two new symbolic database pointers, <em>uniProt</em> and <em>proteome</em>, have been created to point to the two new databases mentioned above. Some parts of our programs use the data in these two DBs. <pre><code>uniProt ---> sp050201 proteome ---> proteins050201</code></pre></li> <li> The existing protein symbolic database pointers, <em>swissProt</em> and <em>proteins</em> remain unchanged. Some parts of our programs still use these two pointers and the data in their associated protein databases. <pre><code>swissProt ---> sp041115 proteins ---> proteins041115</code></pre></li> <li> Two new tables, <em>spOldNew</em> and <em>uniProtAlias</em>, have been added to the proteome database.<br><br> The <em>spOldNew</em> table contains three columns: <ul> <li><em>acc</em> -- primary accession number</li> <li><em>oldDisplayId</em> -- old display ID</li> <li><em>newDisplayId</em> -- new display ID</li> </ul> <br> The uniProtAlias table contains four columns: <ul> <li><em>acc</em> -- UniProt accession number</li> <li><em>alias</em> -- alias (could be acc, old and new display IDs, etc.)</li> <li><em>aliasSrc</em> -- source of the alias type</li> <li><em>aliasSrcDate</em> -- date of the source data</li> </ul> <p> The aliases include primary accessions, secondary accessions new display IDs, old display IDs, and old display IDs corresponding to new secondary accessions.</p> <li> Three new functions have been added to <em>kent/src/hg/spDb.c</em>: <pre><code>char *oldSpDisplayId(char *newSpDisplayId); /* Convert from new Swiss-Prot display ID to old display ID */ char *newSpDisplayId(char *oldSpDisplayId); /* Convert from old Swiss-Prot display ID to new display ID */ char *uniProtFindPrimAcc(char *id); /* Return primary accession given an alias. */</code></pre> The <em>uniProtFindPrimAcc()</em> function is enabled by the new <em>uniProtAlias</em> table.</li> </ol> <p> We anticipate additional changes down the road and may eventually merge the two sets of protein DB pointers into one set.</p> <p> Currently, the <em>proteinID</em> field of the knownGene table for existing genome releases (hg15, hg16, hg17, mm3, mm4, mm5, rn2, and rn3) uses old Swiss-Prot/TrEMBL display IDs (pre-1 Feb. '05). In the future, we may change this field to show the UniProt accession number. Should we choose not to change the content of the <em>proteinID</em> field, we may consider adding a new field, <em>uniProtAcc</em>.</p> <p> If you have any questions about these changes and their impact on your work, please email us at <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. Mirror sites may send questions to <a href="mailto:genome-mirror@soe.ucsc.edu">genome-mirror@soe.ucsc.edu</a>. <strong><em><span class="gbsWarnText">Messages sent to these addresses will be posted to the moderated mailing lists, which are archived on a SEARCHABLE, PUBLIC <a HREF="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror">Google Groups forum</a></span></em></strong>.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->