Fr3 conservation alignment: Difference between revisions
From genomewiki
Jump to navigationJump to search
(details complete) |
(updated to 8-way) |
||
| (One intermediate revision by the same user not shown) | |||
| Line 2: | Line 2: | ||
<UL> | <UL> | ||
<LI>Fugu | <LI>Fugu 8-way [[Fr3 Genome size statistics]]</LI> | ||
<LI>Fugu | <LI>Fugu 8-way [[Fr3 conservation lastz parameters]]</LI> | ||
<LI>all other [[UCSC Multiple Alignments]]</LI> | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
| Line 53: | Line 53: | ||
<TD>2011-12-02</TD><TD ALIGN=RIGHT>55.527%</TD> | <TD>2011-12-02</TD><TD ALIGN=RIGHT>55.527%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://dolphin.lab.nig.ac.jp/medaka/index.php | <TH>[http://www.ncbi.nlm.nih.gov/genome/2661 05]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=gadMor1 gadMor1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CAEA00 Gadus<BR>morhua]</TD><TD>Atlantic cod</TD> | ||
<TD>May. 2010 (Genofisk GadMor_May2010/gadMor1)</TD> | |||
<TD>Genofisk GadMor_May2010 (GCA_000231765.1)</TD> | |||
<TD ALIGN=RIGHT>2011-12-29</TD> | |||
<TD ALIGN=RIGHT>2012-01-04</TD> | |||
<TD>2012-01-14</TD><TD ALIGN=RIGHT>30.327%</TD> | |||
</TR><TR> | |||
<TH>[http://dolphin.lab.nig.ac.jp/medaka/index.php 06]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=oryLat2 oryLat2]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=BAAE01 Oryzias<BR>latipes]</TD><TD>Medaka</TD> | |||
<TD>Oct. 2005 (NIG/UT MEDAKA1/oryLat2)</TD> | <TD>Oct. 2005 (NIG/UT MEDAKA1/oryLat2)</TD> | ||
<TD>NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000)</TD> | <TD>NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000)</TD> | ||
| Line 60: | Line 67: | ||
<TD>2011-12-02</TD><TD ALIGN=RIGHT>43.863%</TD> | <TD>2011-12-02</TD><TD ALIGN=RIGHT>43.863%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Danio_rerio/Zv9/ | <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Danio_rerio/Zv9/ 07]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer7 danRer7]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABZ00 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> | ||
| Line 66: | Line 73: | ||
<TD ALIGN=RIGHT>N/A</TD> | <TD ALIGN=RIGHT>N/A</TD> | ||
<TD>2011-12-02</TD><TD ALIGN=RIGHT>22.823%</TD> | <TD>2011-12-02</TD><TD ALIGN=RIGHT>22.823%</TD> | ||
</TR><TR> | |||
<TH>[http://www.ncbi.nlm.nih.gov/bioproject/56111 08]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=latCha1 latCha1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AFYH00 Latimeria<BR>chalumnae]</TD><TD>Coelacanth</TD> | |||
<TD>Aug. 2011 (LatCha1/latCha1)</TD> | |||
<TD>Broad LatCha1 (GCA_000225785.1)</TD> | |||
<TD ALIGN=RIGHT>2012-01-11</TD> | |||
<TD ALIGN=RIGHT>2012-01-12</TD> | |||
<TD>2012-01-13</TD><TD ALIGN=RIGHT>13.735%</TD> | |||
</TR> | </TR> | ||
</TABLE> | </TABLE> | ||
Latest revision as of 22:26, 29 February 2012
see also
- Fugu 8-way Fr3 Genome size statistics
- Fugu 8-way Fr3 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-preview browser |
Scientific name/ assembly information |
Common name |
assembly date | source version |
Repeat Masker |
Window Masker |
chain on fr3 |
% of fr3 matched (chainLink table) |
|---|---|---|---|---|---|---|---|---|---|
| 01 | fr3 | Takifugu Rubripes | Fugu | Oct. 2011 (FUGU5/fr3) | Fugu Genome Sequencing Consortium - FUGU5 (NCBI project 1434, GCA_000180615.2) | 2011-11-16 | 2011-11-17 | N/A | N/A |
| 02 | tetNig2 | Tetraodon nigroviridis | Tetraodon | Mar. 2007 (Genoscope 8.0/tetNig2) | Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000) | 2010-06-07 | 2009-09-02 | 2011-12-01 | 70.912% |
| 03 | oreNil1 | Oreochromis niloticus | Nile tilapia | Jan. 2011 (Nile tilapia/oreNil1) | Broad Institute of MIT and Harvard Orenil1.0 (GCA_000188235.1) | 2011-11-30 | 2011-11-30 | 2011-12-02 | 57.240% |
| 04 | gasAcu1 | Gasterosteus aculeatus | Stickleback | Feb. 2006 (Broad/gasAcu1) | Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000) | 2009-08-15 | 2009-08-15 | 2011-12-02 | 55.527% |
| 05 | gadMor1 | Gadus morhua | Atlantic cod | May. 2010 (Genofisk GadMor_May2010/gadMor1) | Genofisk GadMor_May2010 (GCA_000231765.1) | 2011-12-29 | 2012-01-04 | 2012-01-14 | 30.327% |
| 06 | oryLat2 | Oryzias latipes | Medaka | Oct. 2005 (NIG/UT MEDAKA1/oryLat2) | NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000) | 2009-08-15 | 2009-08-15 | 2011-12-02 | 43.863% |
| 07 | danRer7 | Danio rerio | Zebrafish | Jul. 2010 (Zv9/danRer7) | Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2) | 2010-12-03 | N/A | 2011-12-02 | 22.823% |
| 08 | latCha1 | Latimeria chalumnae | Coelacanth | Aug. 2011 (LatCha1/latCha1) | Broad LatCha1 (GCA_000225785.1) | 2012-01-11 | 2012-01-12 | 2012-01-13 | 13.735% |
