Ce10 conservation alignment: Difference between revisions
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<UL> | <UL> | ||
<LI>June 2011 C. elegans 9-way [[Ce10 Genome size statistics]]</LI> | <LI>June 2011 C. elegans 9-way [[Ce10 Genome size statistics]]</LI> | ||
<LI>June 2011 C. elegans 9-way [[Ce10_conservation_lastz_parameters]]<LI> | <LI>June 2011 C. elegans 9-way [[Ce10_conservation_lastz_parameters]]</LI> | ||
<LI>all other [[UCSC Multiple Alignments]]</LI> | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
==UCSC and external download locations== | |||
<TABLE BORDER=1> | |||
<TR><TH>UCSC download locations</TH><TH>external source locations</TH></TR> | |||
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/ce10/ elegans]</TD><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS220/genomes/c_elegans/ WormBase WS220]</TD></TR> | |||
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/cb4/ briggsae]</TD><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS220/genomes/c_briggsae/ WormBase WS225]</TD></TR> | |||
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caePb3/ brenneri]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_brenneri/C_brenneri-6.0.1b/ Genbank 6.0.1b]</TD></TR> | |||
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeJap4/ japonica]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_japonica/C_japonica-7.0.1/ Genbank 7.0.1]</TD></TR> | |||
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeAng1/ angaria]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_PS1010/ps1010rel4/ Genbank ps1010rel4]</TD></TR> | |||
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeRem4/ remanei]</TD><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS220/genomes/c_remanei/ WormBase WS220]</TD></TR> | |||
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeSp71/ C. sp. 7 JU1286]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_7_MAF_2007/Caenorhabditis_sp7_JU1286-4.0.1/ Genbank 4.0.1]</TD></TR> | |||
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeSp91/ C. sp. 9 JU1422]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ Genbank 3.0.1]</TD></TR> | |||
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeSp111/ C. sp. 11 JU1373]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_11_MAF_2010/Caenorhabditis_sp11_JU1373-3.0.1/ Genbank 3.0.1]</TD></TR> | |||
</TABLE> | |||
Please note, the external sources often provide several different types of names for contigs and scaffolds. When these sequences are placed in the UCSC genome browser a choice is made for the format of the names. If you want to display custom tracks on the UCSC genome browser, you will need to use the UCSC contig/scaffold/chromosome naming scheme. | |||
==do not edit== | ==do not edit== | ||
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<TR> | <TR> | ||
<TH>URL to<BR>assembly<BR>sequence</TH> | <TH>URL to<BR>assembly<BR>sequence</TH> | ||
<TH>UCSC db name/<BR>genome- | <TH>UCSC db name/<BR>genome-preview<BR>browser</TH> | ||
<TD>Scientific name/<BR>assembly information</TD> | <TD>Scientific name/<BR>assembly information</TD> | ||
<TD>Common<BR>name</TD> | <TD>Common<BR>name</TD> | ||
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</TR> | </TR> | ||
<TR> | <TR> | ||
<TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/ 01]</TH><TH>[http://genome- | <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/ 01]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ce10 ce10]</TH><TD>[http://wiki.wormbase.org/index.php/Caenorhabditis_elegans Caenorhabditis<BR>elegans]</TD><TD>C. elegans</TD> | ||
<TD>Oct. 2010 (WS220/ce10)</TD> | <TD>Oct. 2010 (WS220/ce10)</TD> | ||
<TD>Washington University School of Medicine GSC and Sanger Institute WS220</TD> | <TD>Washington University School of Medicine GSC and Sanger Institute WS220</TD> | ||
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<TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD> | <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS225/genomes/c_briggsae/ 02]</TH><TH>[http://genome- | <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS225/genomes/c_briggsae/ 02]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=cb4 cb4]</TH><TD>[http://www.sanger.ac.uk/Projects/C_briggsae/ Caenorhabditis<BR>briggsae]</TD><TD>C. briggsae</TD> | ||
<TD>Apr. 2011 (WS225/cb4)</TD> | <TD>Apr. 2011 (WS225/cb4)</TD> | ||
<TD>Washington University School of Medicine GSC and Sanger Institute cb4 </TD> | <TD>Washington University School of Medicine GSC and Sanger Institute cb4 </TD> | ||
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<TD>2011-06-07</TD><TD ALIGN=RIGHT>39.386%</TD> | <TD>2011-06-07</TD><TD ALIGN=RIGHT>39.386%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 03]</TH><TH>[http://genome- | <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 03]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp91 caeSp91]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENM01 Caenorhabditis<BR>sp9.<BR>JU1422]</TD><TD>C. sp. 9 ju1422</TD> | ||
<TD>Nov. 2010 (WUSTL 3.0.1/caeSp91)</TD> | <TD>Nov. 2010 (WUSTL 3.0.1/caeSp91)</TD> | ||
<TD>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186805.1)</TD> | <TD>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186805.1)</TD> | ||
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<TD>2011-06-07</TD><TD ALIGN=RIGHT>42.169%</TD> | <TD>2011-06-07</TD><TD ALIGN=RIGHT>42.169%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_remanei/ 04]</TH><TH>[http://genome- | <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_remanei/ 04]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeRem4 caeRem4]</TH><TD>[http://genome.wustl.edu/genomes/view/caenorhabditis_remanei/ Caenorhabditis<BR>remanei]</TD><TD>C. remanei</TD> | ||
<TD>Jul. 2007 (WS220/caeRem4)</TD> | <TD>Jul. 2007 (WS220/caeRem4)</TD> | ||
<TD>Washington University School of Medicine GSC C. remanei 15.0.1</TD> | <TD>Washington University School of Medicine GSC C. remanei 15.0.1</TD> | ||
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<TD>2011-06-07</TD><TD ALIGN=RIGHT>41.722%</TD> | <TD>2011-06-07</TD><TD ALIGN=RIGHT>41.722%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 05]</TH><TH>[http://genome- | <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 05]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp111 caeSp111]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEKS01 Caenorhabditis<BR>sp.<BR>11<BR>JU1373]</TD><TD>C. sp. 11 ju1373</TD> | ||
<TD>Nov. 2010 (WUSTL 3.0.1/caeSp111)</TD> | <TD>Nov. 2010 (WUSTL 3.0.1/caeSp111)</TD> | ||
<TD>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186765.1)</TD> | <TD>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186765.1)</TD> | ||
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<TD>2011-06-07</TD><TD ALIGN=RIGHT>37.876%</TD> | <TD>2011-06-07</TD><TD ALIGN=RIGHT>37.876%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_brenneri/C_brenneri-6.0.1b/ 06]</TH><TH>[http://genome- | <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_brenneri/C_brenneri-6.0.1b/ 06]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caePb3 caePb3]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABEG02 Caenorhabditis<BR>brenneri]</TD><TD>C. brenneri</TD> | ||
<TD>Nov. 2010 (C. brenneri 6.0.1b/caePb3)</TD> | <TD>Nov. 2010 (C. brenneri 6.0.1b/caePb3)</TD> | ||
<TD>The Caenorhabditis brenneri Sequencing and Analysis Consortium (GCA_000143925.2)</TD> | <TD>The Caenorhabditis brenneri Sequencing and Analysis Consortium (GCA_000143925.2)</TD> | ||
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<TD>2011-06-08</TD><TD ALIGN=RIGHT>40.644%</TD> | <TD>2011-06-08</TD><TD ALIGN=RIGHT>40.644%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_7_MAF_2007/Caenorhabditis_sp7_JU1286-4.0.1/ 07]</TH><TH>[http://genome- | <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_7_MAF_2007/Caenorhabditis_sp7_JU1286-4.0.1/ 07]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp71 caeSp71]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENL01 Caenorhabditis<BR>sp7.<BR>JU1286]</TD><TD>C. sp. 7 ju1286</TD> | ||
<TD>Nov. 2010 (WUSTL 4.0.1/caeSp71)</TD> | <TD>Nov. 2010 (WUSTL 4.0.1/caeSp71)</TD> | ||
<TD>Washington University School of Medicine GSC Caenorhabditis sp. 7 JU1286 MAF-2007 4.0.1 (GCA_000186785.1)</TD> | <TD>Washington University School of Medicine GSC Caenorhabditis sp. 7 JU1286 MAF-2007 4.0.1 (GCA_000186785.1)</TD> | ||
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<TD>2011-06-07</TD><TD ALIGN=RIGHT>40.236%</TD> | <TD>2011-06-07</TD><TD ALIGN=RIGHT>40.236%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_japonica/C_japonica-7.0.1/ 08]</TH><TH>[http://genome- | <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_japonica/C_japonica-7.0.1/ 08]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeJap4 caeJap4]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABLE03 Caenorhabditis<BR>japonica]</TD><TD>C. japonica</TD> | ||
<TD>Aug. 2010 (WUSTL 7.0.1/caeJap4)</TD> | <TD>Aug. 2010 (WUSTL 7.0.1/caeJap4)</TD> | ||
<TD>Washington University School of Medicine GSC C. japonica 7.0.1 (GCA_000147155.1)</TD> | <TD>Washington University School of Medicine GSC C. japonica 7.0.1 (GCA_000147155.1)</TD> | ||
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<TD>2011-06-07</TD><TD ALIGN=RIGHT>27.737%</TD> | <TD>2011-06-07</TD><TD ALIGN=RIGHT>27.737%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_PS1010/ps1010rel4/ 09]</TH><TH>[http://genome- | <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_PS1010/ps1010rel4/ 09]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeAng1 caeAng1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEHI01 Caenorhabditis<BR>angaria]</TD><TD>C. angaria</TD> | ||
<TD>Oct. 2010 (WS225/caeAng1)</TD> | <TD>Oct. 2010 (WS225/caeAng1)</TD> | ||
<TD>Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1)</TD> | <TD>Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1)</TD> | ||
Latest revision as of 15:34, 13 June 2011
see also
- June 2011 C. elegans 9-way Ce10 Genome size statistics
- June 2011 C. elegans 9-way Ce10_conservation_lastz_parameters
- all other UCSC Multiple Alignments
UCSC and external download locations
| UCSC download locations | external source locations |
|---|---|
| elegans | WormBase WS220 |
| briggsae | WormBase WS225 |
| brenneri | Genbank 6.0.1b |
| japonica | Genbank 7.0.1 |
| angaria | Genbank ps1010rel4 |
| remanei | WormBase WS220 |
| C. sp. 7 JU1286 | Genbank 4.0.1 |
| C. sp. 9 JU1422 | Genbank 3.0.1 |
| C. sp. 11 JU1373 | Genbank 3.0.1 |
Please note, the external sources often provide several different types of names for contigs and scaffolds. When these sequences are placed in the UCSC genome browser a choice is made for the format of the names. If you want to display custom tracks on the UCSC genome browser, you will need to use the UCSC contig/scaffold/chromosome naming scheme.
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-preview browser |
Scientific name/ assembly information |
Common name |
assembly date | source version |
Repeat Masker |
Window Masker |
chain on ce10 |
% of ce10 matched (chainLink table) |
|---|---|---|---|---|---|---|---|---|---|
| 01 | ce10 | Caenorhabditis elegans | C. elegans | Oct. 2010 (WS220/ce10) | Washington University School of Medicine GSC and Sanger Institute WS220 | 2011-05-23 | N/A | N/A | N/A |
| 02 | cb4 | Caenorhabditis briggsae | C. briggsae | Apr. 2011 (WS225/cb4) | Washington University School of Medicine GSC and Sanger Institute cb4 | 2011-05-24 | 2011-05-24 | 2011-06-07 | 39.386% |
| 03 | caeSp91 | Caenorhabditis sp9. JU1422 | C. sp. 9 ju1422 | Nov. 2010 (WUSTL 3.0.1/caeSp91) | Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186805.1) | 2011-05-27 | 2011-05-31 | 2011-06-07 | 42.169% |
| 04 | caeRem4 | Caenorhabditis remanei | C. remanei | Jul. 2007 (WS220/caeRem4) | Washington University School of Medicine GSC C. remanei 15.0.1 | 2011-05-25 | 2011-05-25 | 2011-06-07 | 41.722% |
| 05 | caeSp111 | Caenorhabditis sp. 11 JU1373 | C. sp. 11 ju1373 | Nov. 2010 (WUSTL 3.0.1/caeSp111) | Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186765.1) | 2011-05-31 | 2011-05-31 | 2011-06-07 | 37.876% |
| 06 | caePb3 | Caenorhabditis brenneri | C. brenneri | Nov. 2010 (C. brenneri 6.0.1b/caePb3) | The Caenorhabditis brenneri Sequencing and Analysis Consortium (GCA_000143925.2) | 2011-06-08 | 2011-06-08 | 2011-06-08 | 40.644% |
| 07 | caeSp71 | Caenorhabditis sp7. JU1286 | C. sp. 7 ju1286 | Nov. 2010 (WUSTL 4.0.1/caeSp71) | Washington University School of Medicine GSC Caenorhabditis sp. 7 JU1286 MAF-2007 4.0.1 (GCA_000186785.1) | 2011-05-27 | 2011-05-27 | 2011-06-07 | 40.236% |
| 08 | caeJap4 | Caenorhabditis japonica | C. japonica | Aug. 2010 (WUSTL 7.0.1/caeJap4) | Washington University School of Medicine GSC C. japonica 7.0.1 (GCA_000147155.1) | 2011-06-03 | 2011-06-03 | 2011-06-07 | 27.737% |
| 09 | caeAng1 | Caenorhabditis angaria | C. angaria | Oct. 2010 (WS225/caeAng1) | Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1) | 2011-05-31 | 2011-05-31 | 2011-06-08 | 17.625% |
