XenTro3 conservation alignment: Difference between revisions
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<LI>X. tropicalis 8-way [[XenTro3 Genome size statistics]]</LI> | <LI>X. tropicalis 8-way [[XenTro3 Genome size statistics]]</LI> | ||
<LI>X. tropicalis 8-way [[XenTro3 conservation lastz parameters]]</LI> | <LI>X. tropicalis 8-way [[XenTro3 conservation lastz parameters]]</LI> | ||
<LI>all other [[UCSC Multiple Alignments]]</LI> | |||
</UL> | |||
==see also== | |||
<UL> | |||
<LI>X. tropicalis 9-way [[XenTro3 Genome size statistics]]</LI> | |||
<LI>X. tropicalis 9-way [[XenTro3 conservation lastz parameters]]</LI> | |||
<LI>all other [[UCSC Multiple Alignments]]</LI> | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
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</TR> | </TR> | ||
<TR> | <TR> | ||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Anolis_carolinensis/ | <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Xenopus_tropicalis/v4.2/ 01]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=xenTro3 xenTro3]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAMC01 Xenopus<BR>tropicalis]</TD><TD>X. tropicalis</TD> | ||
<TD>Nov. 2009 (JGI 4.2/xenTro3)</TD> | |||
<TD>US DOE Joint Genome Institute (JGI-PGF) (GCA_000004195.1)</TD> | |||
<TD ALIGN=RIGHT>2011-09-08</TD> | |||
<TD ALIGN=RIGHT>2011-09-08</TD> | |||
<TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD> | |||
</TR><TR> | |||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Anolis_carolinensis/ 02]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=anoCar2 anoCar2]</TH><TD>[http://www.broadinstitute.org/models/anole Anolis<BR>carolinensis]</TD><TD>Lizard</TD> | |||
<TD>May 2010 (Broad AnoCar2.0/anoCar2)</TD> | <TD>May 2010 (Broad AnoCar2.0/anoCar2)</TD> | ||
<TD>Broad Institute of MIT and Harvard AnoCar 2.0 (GCA_000090745.1)</TD> | <TD>Broad Institute of MIT and Harvard AnoCar 2.0 (GCA_000090745.1)</TD> | ||
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<TD>2011-09-20</TD><TD ALIGN=RIGHT>6.775%</TD> | <TD>2011-09-20</TD><TD ALIGN=RIGHT>6.775%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://genome.wustl.edu/pub/organism/Other_Vertebrates/Gallus_gallus/assembly/Gallus_gallus-3.0/ | <TH>[http://genome.wustl.edu/pub/organism/Other_Vertebrates/Gallus_gallus/assembly/Gallus_gallus-3.0/ 03]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal3 galGal3]</TH><TD>[http://genome.wustl.edu/genomes/view/gallus_gallus/ Gallus<BR>gallus]</TD><TD>Chicken</TD> | ||
<TD>May 2006 (WUGSC 2.1/galGal3)</TD> | <TD>May 2006 (WUGSC 2.1/galGal3)</TD> | ||
<TD>Chicken Genome Sequencing Consortium May 2006 release</TD> | <TD>Chicken Genome Sequencing Consortium May 2006 release</TD> | ||
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<TD>2011-09-20</TD><TD ALIGN=RIGHT>4.730%</TD> | <TD>2011-09-20</TD><TD ALIGN=RIGHT>4.730%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Meleagris_gallopavo/Turkey_2.01/ | <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Meleagris_gallopavo/Turkey_2.01/ 04]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melGal1 melGal1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Meleagris_gallopavo/Turkey_2.01/ Meleagris<BR>gallopavo]</TD><TD>Turkey</TD> | ||
<TD>Dec. 2009 (TGC Turkey_2.01/melGal1)</TD> | <TD>Dec. 2009 (TGC Turkey_2.01/melGal1)</TD> | ||
<TD>TGC (NCBI Project ID: 10805, Accession: GCA_000146605.1)</TD> | <TD>TGC (NCBI Project ID: 10805, Accession: GCA_000146605.1)</TD> | ||
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<TD>2011-09-23</TD><TD ALIGN=RIGHT>3.120%</TD> | <TD>2011-09-23</TD><TD ALIGN=RIGHT>3.120%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://www.broadinstitute.org/mammals/opossum | <TH>[http://www.broadinstitute.org/mammals/opossum 05]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 monDom5]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAFR03 Monodelphis<BR>domestica]</TD><TD>Opossum</TD> | ||
<TD>Oct. 2006 (Broad/monDom5)</TD> | <TD>Oct. 2006 (Broad/monDom5)</TD> | ||
<TD>Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000)</TD> | <TD>Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000)</TD> | ||
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<TD>2011-09-23</TD><TD ALIGN=RIGHT>5.492%</TD> | <TD>2011-09-23</TD><TD ALIGN=RIGHT>5.492%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://www.hgsc.bcm.tmc.edu/project-species-m-Rat.hgsc?pageLocation=Rat | <TH>[http://www.hgsc.bcm.tmc.edu/project-species-m-Rat.hgsc?pageLocation=Rat 06]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rn4 rn4]</TH><TD>[http://www.hgsc.bcm.tmc.edu/project-species-m-Rat.hgsc?pageLocation=Rat Rattus<BR>norvegicus]</TD><TD>Rat</TD> | ||
<TD>Nov. 2004 (Baylor 3.4/rn4)</TD> | <TD>Nov. 2004 (Baylor 3.4/rn4)</TD> | ||
<TD>Baylor HGSC v. 3.4</TD> | <TD>Baylor HGSC v. 3.4</TD> | ||
| Line 60: | Line 75: | ||
<TD>2011-09-23</TD><TD ALIGN=RIGHT>5.216%</TD> | <TD>2011-09-23</TD><TD ALIGN=RIGHT>5.216%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/index.shtml | <TH>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/index.shtml 07]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9 mm9]</TH><TD>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/index.shtml Mus<BR>musculus]</TD><TD>Mouse</TD> | ||
<TD>July 2007 (NCBI37/mm9)</TD> | <TD>July 2007 (NCBI37/mm9)</TD> | ||
<TD>NCBI Build 37</TD> | <TD>NCBI Build 37</TD> | ||
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<TD>2011-09-21</TD><TD ALIGN=RIGHT>6.609%</TD> | <TD>2011-09-21</TD><TD ALIGN=RIGHT>6.609%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml | <TH>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml 08]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hg19 hg19]</TH><TD>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml Homo<BR>sapiens]</TD><TD>Human</TD> | ||
<TD>Feb. 2009 (GRCh37/hg19)</TD> | <TD>Feb. 2009 (GRCh37/hg19)</TD> | ||
<TD>GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)</TD> | <TD>GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)</TD> | ||
| Line 74: | Line 89: | ||
<TD>2011-09-21</TD><TD ALIGN=RIGHT>6.694%</TD> | <TD>2011-09-21</TD><TD ALIGN=RIGHT>6.694%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://www.sanger.ac.uk/Projects/D_rerio/Zv9_assembly_information.shtml | <TH>[http://www.sanger.ac.uk/Projects/D_rerio/Zv9_assembly_information.shtml 09]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer7 danRer7]</TH><TD>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/zebrafish/index.shtml Danio<BR>rerio]</TD><TD>Zebrafish</TD> | ||
<TD>Jul. 2010 (Zv9/danRer7)</TD> | <TD>Jul. 2010 (Zv9/danRer7)</TD> | ||
<TD>Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2)</TD> | <TD>Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2)</TD> | ||
Revision as of 23:49, 23 September 2011
see also
- X. tropicalis 8-way XenTro3 Genome size statistics
- X. tropicalis 8-way XenTro3 conservation lastz parameters
- all other UCSC Multiple Alignments
see also
- X. tropicalis 9-way XenTro3 Genome size statistics
- X. tropicalis 9-way XenTro3 conservation lastz parameters
- all other UCSC Multiple Alignments
do not edit
This table is automatically generated off-line from the UCSC databases. Please do not edit it.
| URL to assembly sequence |
UCSC db name/ genome-test browser |
Scientific name/ assembly information |
Common name |
assembly date | source version |
Repeat Masker |
Window Masker |
chain on xenTro3 |
% of xenTro3 matched (chainLink table) |
|---|---|---|---|---|---|---|---|---|---|
| 01 | xenTro3 | Xenopus tropicalis | X. tropicalis | Nov. 2009 (JGI 4.2/xenTro3) | US DOE Joint Genome Institute (JGI-PGF) (GCA_000004195.1) | 2011-09-08 | 2011-09-08 | N/A | N/A |
| 02 | anoCar2 | Anolis carolinensis | Lizard | May 2010 (Broad AnoCar2.0/anoCar2) | Broad Institute of MIT and Harvard AnoCar 2.0 (GCA_000090745.1) | 2011-04-12 | 2011-04-13 | 2011-09-20 | 6.775% |
| 03 | galGal3 | Gallus gallus | Chicken | May 2006 (WUGSC 2.1/galGal3) | Chicken Genome Sequencing Consortium May 2006 release | 2009-08-15 | 2007-01-02 | 2011-09-20 | 4.730% |
| 04 | melGal1 | Meleagris gallopavo | Turkey | Dec. 2009 (TGC Turkey_2.01/melGal1) | TGC (NCBI Project ID: 10805, Accession: GCA_000146605.1) | 2010-11-04 | N/A | 2011-09-23 | 3.120% |
| 05 | monDom5 | Monodelphis domestica | Opossum | Oct. 2006 (Broad/monDom5) | Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000) | 2009-08-14 | 2009-08-14 | 2011-09-23 | 5.492% |
| 06 | rn4 | Rattus norvegicus | Rat | Nov. 2004 (Baylor 3.4/rn4) | Baylor HGSC v. 3.4 | 2009-08-15 | N/A | 2011-09-23 | 5.216% |
| 07 | mm9 | Mus musculus | Mouse | July 2007 (NCBI37/mm9) | NCBI Build 37 | 2009-08-14 | N/A | 2011-09-21 | 6.609% |
| 08 | hg19 | Homo sapiens | Human | Feb. 2009 (GRCh37/hg19) | GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1) | 2009-08-15 | N/A | 2011-09-21 | 6.694% |
| 09 | danRer7 | Danio rerio | Zebrafish | Jul. 2010 (Zv9/danRer7) | Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2) | 2010-12-03 | N/A | 2011-09-21 | 7.107% |
