Ce11 26-way conservation alignment: Difference between revisions

From genomewiki
Jump to navigationJump to search
No edit summary
(add reference to pair-wise matrix)
 
(2 intermediate revisions by the same user not shown)
Line 5: Line 5:
<LI>C.&nbsp;elegans 26-way [[Ce11 26-way conservation lastz parameters]]</LI>
<LI>C.&nbsp;elegans 26-way [[Ce11 26-way conservation lastz parameters]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>see also: [[Ws245ChainNet|matrix]] of all pair-wise alignments
</UL>
</UL>


Line 32: Line 33:
   <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>[http://www.wormbase.org/species/c_sp5 02]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp51 caeSp51]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA194557/ Caenorhabditis<BR>sp5<BR>ju800]</TD><TD>C.&nbsp;sp.&nbsp;5&nbsp;ju800</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA194557/ 02]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp51 caeSp51]</TH><TD>[http://www.wormbase.org/species/c_sp5 Caenorhabditis<BR>sp5<BR>ju800]</TD><TD>C.&nbsp;sp.&nbsp;5&nbsp;ju800</TD>
   <TD>Jan.&nbsp;2012&nbsp;(WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51)</TD>
   <TD>Jan.&nbsp;2012&nbsp;(WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51)</TD>
   <TD>University of Edinburgh Caenorhabditis sp. 5 genome project</TD>
   <TD>University of Edinburgh Caenorhabditis sp. 5 genome project</TD>
Line 53: Line 54:
   <TD>2015-07-02</TD><TD ALIGN=RIGHT>41.715%</TD>
   <TD>2015-07-02</TD><TD ALIGN=RIGHT>41.715%</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS225/genomes/c_briggsae/ 05]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=cb4 cb4]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS225/genomes/c_briggsae/ Caenorhabditis<BR>briggsae]</TD><TD>C.&nbsp;briggsae</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS225/genomes/c_briggsae/ 05]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=cb4 cb4]</TH><TD>[http://www.wormbase.org/species/c_briggsae Caenorhabditis<BR>briggsae]</TD><TD>C.&nbsp;briggsae</TD>
   <TD>Apr.&nbsp;2011&nbsp;(WS225/cb4)</TD>
   <TD>Apr.&nbsp;2011&nbsp;(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>
Line 60: Line 61:
   <TD>2015-07-01</TD><TD ALIGN=RIGHT>39.384%</TD>
   <TD>2015-07-01</TD><TD ALIGN=RIGHT>39.384%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000186765.1 06]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp111 caeSp111]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Caenorhabditis_sp._11_KK-2011/all_assembly_versions/GCA_000186765.1_Caenorhabditis_sp11_JU1373-3.0.1/ Caenorhabditis<BR>tropicalis]</TD><TD>C.&nbsp;tropicalis</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Caenorhabditis_sp._11_KK-2011/all_assembly_versions/GCA_000186765.1_Caenorhabditis_sp11_JU1373-3.0.1/ 06]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp111 caeSp111]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000186765.1 Caenorhabditis<BR>tropicalis]</TD><TD>C.&nbsp;tropicalis</TD>
   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;3.0.1/caeSp111)</TD>
   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;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>
Line 67: Line 68:
   <TD>2015-07-07</TD><TD ALIGN=RIGHT>37.870%</TD>
   <TD>2015-07-07</TD><TD ALIGN=RIGHT>37.870%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000147155.1 07]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeJap4 caeJap4]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Caenorhabditis_japonica/all_assembly_versions/GCA_000147155.1_C_japonica-7.0.1/ Caenorhabditis<BR>japonica]</TD><TD>C.&nbsp;japonica</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Caenorhabditis_japonica/all_assembly_versions/GCA_000147155.1_C_japonica-7.0.1/ 07]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeJap4 caeJap4]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000147155.1/ Caenorhabditis<BR>japonica]</TD><TD>C.&nbsp;japonica</TD>
   <TD>Aug.&nbsp;2010&nbsp;(WUSTL&nbsp;7.0.1/caeJap4)</TD>
   <TD>Aug.&nbsp;2010&nbsp;(WUSTL&nbsp;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>
Line 74: Line 75:
   <TD>2015-06-25</TD><TD ALIGN=RIGHT>27.709%</TD>
   <TD>2015-06-25</TD><TD ALIGN=RIGHT>27.709%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/c_angaria 08]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeAng2 caeAng2]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA51225/ Caenorhabditis<BR>angaria]</TD><TD>C.&nbsp;angaria</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA51225/ 08]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeAng2 caeAng2]</TH><TD>[http://www.wormbase.org/species/c_angaria Caenorhabditis<BR>angaria]</TD><TD>C.&nbsp;angaria</TD>
   <TD>Mar.&nbsp;2012&nbsp;(WS245/caeAng2)</TD>
   <TD>Mar.&nbsp;2012&nbsp;(WS245/caeAng2)</TD>
   <TD>Division of Biology, California Institute of Technology</TD>
   <TD>Division of Biology, California Institute of Technology</TD>
Line 81: Line 82:
   <TD>2015-06-30</TD><TD ALIGN=RIGHT>17.682%</TD>
   <TD>2015-06-30</TD><TD ALIGN=RIGHT>17.682%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/p_pacificus 09]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=priPac3 priPac3]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA12644/ Pristionchus<BR>pacificus]</TD><TD>P.&nbsp;pacificus</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA12644/ 09]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=priPac3 priPac3]</TH><TD>[http://www.wormbase.org/species/p_pacificus Pristionchus<BR>pacificus]</TD><TD>P.&nbsp;pacificus</TD>
   <TD>Aug.&nbsp;2014&nbsp;(P_pacificus-v2/priPac3)</TD>
   <TD>Aug.&nbsp;2014&nbsp;(P_pacificus-v2/priPac3)</TD>
   <TD>Max Planck Institute for Developmental Biology P. pacificus genome project</TD>
   <TD>Max Planck Institute for Developmental Biology P. pacificus genome project</TD>
Line 88: Line 89:
   <TD>2015-07-01</TD><TD ALIGN=RIGHT>6.308%</TD>
   <TD>2015-07-01</TD><TD ALIGN=RIGHT>6.308%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/p_exspectatus 10]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=priExs1 priExs1]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEB6009/ Pristionchus<BR>exspectatus]</TD><TD>P.&nbsp;exspectatus</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEB6009/ 10]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=priExs1 priExs1]</TH><TD>[http://www.wormbase.org/species/p_exspectatus Pristionchus<BR>exspectatus]</TD><TD>P.&nbsp;exspectatus</TD>
   <TD>Mar.&nbsp;2014&nbsp;(WS243/P_exspectatus_v1/priExs1)</TD>
   <TD>Mar.&nbsp;2014&nbsp;(WS243/P_exspectatus_v1/priExs1)</TD>
   <TD>Max Planck Institite for Developmental Genetics</TD>
   <TD>Max Planck Institite for Developmental Genetics</TD>
Line 95: Line 96:
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>6.222%</TD>
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>6.222%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/b_xylophilus 11]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=burXyl1 burXyl1]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEA64437/ Bursaphelenchus<BR>xylophilus]</TD><TD>Pine&nbsp;wood&nbsp;nematode</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEA64437/ 11]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=burXyl1 burXyl1]</TH><TD>[http://www.wormbase.org/species/b_xylophilus Bursaphelenchus<BR>xylophilus]</TD><TD>Pine&nbsp;wood&nbsp;nematode</TD>
   <TD>Nov.&nbsp;2011&nbsp;(WS229/B.&nbsp;xylophilus&nbsp;Ka4C1/burXyl1)</TD>
   <TD>Nov.&nbsp;2011&nbsp;(WS229/B.&nbsp;xylophilus&nbsp;Ka4C1/burXyl1)</TD>
   <TD>Wellcome Trust Sanger Institute B. xylophilus genome project</TD>
   <TD>Wellcome Trust Sanger Institute B. xylophilus genome project</TD>
Line 102: Line 103:
   <TD>2015-07-09</TD><TD ALIGN=RIGHT>6.291%</TD>
   <TD>2015-07-09</TD><TD ALIGN=RIGHT>6.291%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000688135.1 12]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ancCey1 ancCey1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ancylostoma_ceylanicum/all_assembly_versions/GCA_000688135.1_Acey_2013.11.30.genDNA/ Ancylostoma<BR>ceylanicum]</TD><TD>A.&nbsp;ceylanicum</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ancylostoma_ceylanicum/all_assembly_versions/GCA_000688135.1_Acey_2013.11.30.genDNA/ 12]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ancCey1 ancCey1]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000688135.1 Ancylostoma<BR>ceylanicum]</TD><TD>A.&nbsp;ceylanicum</TD>
   <TD>Mar.&nbsp;2014&nbsp;(WS243/Acey_2013.11.30.genDNA/ancCey1)</TD>
   <TD>Mar.&nbsp;2014&nbsp;(WS243/Acey_2013.11.30.genDNA/ancCey1)</TD>
   <TD>Cornell University Ancylostoma ceylanicum genome project</TD>
   <TD>Cornell University Ancylostoma ceylanicum genome project</TD>
Line 109: Line 110:
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>9.736%</TD>
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>9.736%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/h_contortus 13]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=haeCon2 haeCon2]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEB506/ Haemonchus<BR>contortus]</TD><TD>Barber&nbsp;pole&nbsp;worm</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEB506/ 13]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=haeCon2 haeCon2]</TH><TD>[http://www.wormbase.org/species/h_contortus Haemonchus<BR>contortus]</TD><TD>Barber&nbsp;pole&nbsp;worm</TD>
   <TD>Jul.&nbsp;2013&nbsp;(WormBase&nbsp;WS239/haeCon2)</TD>
   <TD>Jul.&nbsp;2013&nbsp;(WormBase&nbsp;WS239/haeCon2)</TD>
   <TD>Sanger Institute</TD>
   <TD>Sanger Institute</TD>
Line 116: Line 117:
   <TD>2015-07-07</TD><TD ALIGN=RIGHT>8.936%</TD>
   <TD>2015-07-07</TD><TD ALIGN=RIGHT>8.936%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000507365.1 14]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=necAme1 necAme1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Necator_americanus/all_assembly_versions/GCA_000507365.1_N_americanus_v1/ Necator<BR>americanus]</TD><TD>N.&nbsp;americanus</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Necator_americanus/all_assembly_versions/GCA_000507365.1_N_americanus_v1/ 14]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=necAme1 necAme1]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000507365.1 Necator<BR>americanus]</TD><TD>N.&nbsp;americanus</TD>
   <TD>Dec.&nbsp;2013&nbsp;(WS242/N_americanus_v1/necAme1)</TD>
   <TD>Dec.&nbsp;2013&nbsp;(WS242/N_americanus_v1/necAme1)</TD>
   <TD>The Genome Institute at Washington University</TD>
   <TD>The Genome Institute at Washington University</TD>
Line 123: Line 124:
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>8.902%</TD>
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>8.902%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/p_redivivus 15]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=panRed1 panRed1]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA186477/ Panagrellus<BR>redivivus]</TD><TD>Microworm</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA186477/ 15]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=panRed1 panRed1]</TH><TD>[http://www.wormbase.org/species/p_redivivus Panagrellus<BR>redivivus]</TD><TD>Microworm</TD>
   <TD>Feb.&nbsp;2013&nbsp;(Pred3/panRed1)</TD>
   <TD>Feb.&nbsp;2013&nbsp;(Pred3/panRed1)</TD>
   <TD>California Institute of Technology P. redivivus genome project</TD>
   <TD>California Institute of Technology P. redivivus genome project</TD>
Line 130: Line 131:
   <TD>2015-07-01</TD><TD ALIGN=RIGHT>6.585%</TD>
   <TD>2015-07-01</TD><TD ALIGN=RIGHT>6.585%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000223415.1/ 16]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=hetBac1 hetBac1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Heterorhabditis_bacteriophora/all_assembly_versions/GCA_000223415.1_Heterorhabditis_bacteriophora-7.0/ Heterorhabditis<BR>bacteriophora]</TD><TD>H.&nbsp;bacteriophora/m31e</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Heterorhabditis_bacteriophora/all_assembly_versions/GCA_000223415.1_Heterorhabditis_bacteriophora-7.0/ 16]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=hetBac1 hetBac1]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000223415.1/ Heterorhabditis<BR>bacteriophora]</TD><TD>H.&nbsp;bacteriophora/m31e</TD>
   <TD>Aug.&nbsp;2011&nbsp;(WS229/H.&nbsp;bacteriophora&nbsp;7.0/hetBac1)</TD>
   <TD>Aug.&nbsp;2011&nbsp;(WS229/H.&nbsp;bacteriophora&nbsp;7.0/hetBac1)</TD>
   <TD>Washington University Genome Sequencing Center Heterorhabditis_bacteriophora-7.0</TD>
   <TD>Washington University Genome Sequencing Center Heterorhabditis_bacteriophora-7.0</TD>
Line 137: Line 138:
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>10.486%</TD>
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>10.486%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000298755.1 17]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ascSuu1 ascSuu1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ascaris_suum/all_assembly_versions/GCA_000298755.1_AscSuum_1.0/ Ascaris<BR>suum]</TD><TD>Pig&nbsp;roundworm</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ascaris_suum/all_assembly_versions/GCA_000298755.1_AscSuum_1.0/ 17]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ascSuu1 ascSuu1]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000298755.1 Ascaris<BR>suum]</TD><TD>Pig&nbsp;roundworm</TD>
   <TD>Sep.&nbsp;2012&nbsp;(WS229/AscSuum_1.0/ascSuu1)</TD>
   <TD>Sep.&nbsp;2012&nbsp;(WS229/AscSuum_1.0/ascSuu1)</TD>
   <TD>Beijing Genomics Institute</TD>
   <TD>Beijing Genomics Institute</TD>
Line 144: Line 145:
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>5.722%</TD>
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>5.722%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_001040885.1/ 18]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=strRat2 strRat2]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Strongyloides_ratti/all_assembly_versions/GCA_001040885.1_S_ratti_ED321/ Strongyloides<BR>ratti]</TD><TD>Threadworm</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Strongyloides_ratti/all_assembly_versions/GCA_001040885.1_S_ratti_ED321/ 18]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=strRat2 strRat2]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCA_001040885.1/ Strongyloides<BR>ratti]</TD><TD>Threadworm</TD>
   <TD>Sep.&nbsp;2014&nbsp;(S.&nbsp;ratti&nbsp;ED321/strRat2)</TD>
   <TD>Sep.&nbsp;2014&nbsp;(S.&nbsp;ratti&nbsp;ED321/strRat2)</TD>
   <TD>Wellcome Trust Sanger Institute S. ratti genome project</TD>
   <TD>Wellcome Trust Sanger Institute S. ratti genome project</TD>
Line 151: Line 152:
   <TD>2015-07-09</TD><TD ALIGN=RIGHT>5.669%</TD>
   <TD>2015-07-09</TD><TD ALIGN=RIGHT>5.669%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000181795.1 19]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=triSpi1 triSpi1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Trichinella_spiralis/all_assembly_versions/GCA_000181795.2_Trichinella_spiralis-3.7.1/ Trichinella<BR>spiralis]</TD><TD>Trichinella</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Trichinella_spiralis/all_assembly_versions/GCA_000181795.2_Trichinella_spiralis-3.7.1/ 19]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=triSpi1 triSpi1]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000181795.1 Trichinella<BR>spiralis]</TD><TD>Trichinella</TD>
   <TD>Jan.&nbsp;2011&nbsp;(WS225/Trichinella_spiralis-3.7.1/triSpi1)</TD>
   <TD>Jan.&nbsp;2011&nbsp;(WS225/Trichinella_spiralis-3.7.1/triSpi1)</TD>
   <TD>WashU School of Medicine T. spiralis genome project</TD>
   <TD>WashU School of Medicine T. spiralis genome project</TD>
Line 158: Line 159:
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>2.848%</TD>
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>2.848%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000701005.1 20]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=triSui1 triSui1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Trichuris_suis/all_assembly_versions/GCA_000701005.1_Tsuis_adult_male_v1.0/ Trichuris<BR>suis]</TD><TD>Whipworm</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Trichuris_suis/all_assembly_versions/GCA_000701005.1_Tsuis_adult_male_v1.0/ 20]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=triSui1 triSui1]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000701005.1 Trichuris<BR>suis]</TD><TD>Whipworm</TD>
   <TD>Jul.&nbsp;2014&nbsp;(WS243/T.&nbsp;suis&nbsp;DCEP-RM93M&nbsp;male/triSui1)</TD>
   <TD>Jul.&nbsp;2014&nbsp;(WS243/T.&nbsp;suis&nbsp;DCEP-RM93M&nbsp;male/triSui1)</TD>
   <TD>University of Melboure T. suis (male) genome project</TD>
   <TD>University of Melboure T. suis (male) genome project</TD>
Line 165: Line 166:
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>2.917%</TD>
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>2.917%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/m_incognita 21]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=melInc2 melInc2]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEA28837/ Meloidogyne<BR>incognita]</TD><TD>M.&nbsp;incognita</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEA28837/ 21]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=melInc2 melInc2]</TH><TD>[http://www.wormbase.org/species/m_incognita Meloidogyne<BR>incognita]</TD><TD>M.&nbsp;incognita</TD>
   <TD>Feb.&nbsp;2008&nbsp;(M.&nbsp;incognita&nbsp;WS245/PRJEA28837/melInc2)</TD>
   <TD>Feb.&nbsp;2008&nbsp;(M.&nbsp;incognita&nbsp;WS245/PRJEA28837/melInc2)</TD>
   <TD>Sanger and Genoscope</TD>
   <TD>Sanger and Genoscope</TD>
Line 172: Line 173:
   <TD>2015-06-30</TD><TD ALIGN=RIGHT>3.516%</TD>
   <TD>2015-06-30</TD><TD ALIGN=RIGHT>3.516%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/m_hapla 22]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=melHap1 melHap1]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS210/genomes/m_hapla/ Meloidogyne<BR>hapla]</TD><TD>M.&nbsp;hapla</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS210/genomes/m_hapla/ 22]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=melHap1 melHap1]</TH><TD>[http://www.wormbase.org/species/m_hapla Meloidogyne<BR>hapla]</TD><TD>M.&nbsp;hapla</TD>
   <TD>Sep.&nbsp;2008&nbsp;(M.&nbsp;hapla&nbsp;VW9&nbsp;WS210/melHap1)</TD>
   <TD>Sep.&nbsp;2008&nbsp;(M.&nbsp;hapla&nbsp;VW9&nbsp;WS210/melHap1)</TD>
   <TD>The Center for the Biology of Nematode Parasitism, N.C. State</TD>
   <TD>The Center for the Biology of Nematode Parasitism, N.C. State</TD>
Line 179: Line 180:
   <TD>2015-06-26</TD><TD ALIGN=RIGHT>3.916%</TD>
   <TD>2015-06-26</TD><TD ALIGN=RIGHT>3.916%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/b_malayi 23]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=bruMal2 bruMal2]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA10729/ Brugia<BR>malayi]</TD><TD>Filarial&nbsp;worm</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA10729/ 23]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=bruMal2 bruMal2]</TH><TD>[http://www.wormbase.org/species/b_malayi Brugia<BR>malayi]</TD><TD>Filarial&nbsp;worm</TD>
   <TD>May.&nbsp;2014&nbsp;(WS244/B_malayi-3.1/bruMal2)</TD>
   <TD>May.&nbsp;2014&nbsp;(WS244/B_malayi-3.1/bruMal2)</TD>
   <TD>University of Pittsburgh B. malayi genome project</TD>
   <TD>University of Pittsburgh B. malayi genome project</TD>
Line 186: Line 187:
   <TD>2015-08-11</TD><TD ALIGN=RIGHT>5.065%</TD>
   <TD>2015-08-11</TD><TD ALIGN=RIGHT>5.065%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000499405.1 24]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=oncVol1 oncVol1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Onchocerca_volvulus/all_assembly_versions/GCA_000499405.1_OVOC001/ Onchocerca<BR>volvulus]</TD><TD>O.&nbsp;volvulus</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Onchocerca_volvulus/all_assembly_versions/GCA_000499405.1_OVOC001/ 24]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=oncVol1 oncVol1]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000499405.1 Onchocerca<BR>volvulus]</TD><TD>O.&nbsp;volvulus</TD>
   <TD>Nov.&nbsp;2013&nbsp;(WS241/O_volvulus_Cameroon_v3/oncVol1)</TD>
   <TD>Nov.&nbsp;2013&nbsp;(WS241/O_volvulus_Cameroon_v3/oncVol1)</TD>
   <TD>Wellcome Trust Sanger Institute O. volvulus genome project</TD>
   <TD>Wellcome Trust Sanger Institute O. volvulus genome project</TD>
Line 193: Line 194:
   <TD>2015-08-10</TD><TD ALIGN=RIGHT>5.193%</TD>
   <TD>2015-08-10</TD><TD ALIGN=RIGHT>5.193%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000183805.3 25]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=loaLoa1 loaLoa1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Loa_loa/all_assembly_versions/GCA_000183805.3_Loa_loa_V3.1/ Loa<BR>loa]</TD><TD>Eye&nbsp;worm</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Loa_loa/all_assembly_versions/GCA_000183805.3_Loa_loa_V3.1/ 25]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=loaLoa1 loaLoa1]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000183805.3 Loa<BR>loa]</TD><TD>Eye&nbsp;worm</TD>
   <TD>Jul.&nbsp;2012&nbsp;(WS235/L_loa_Cameroon_isolate/loaLoa1)</TD>
   <TD>Jul.&nbsp;2012&nbsp;(WS235/L_loa_Cameroon_isolate/loaLoa1)</TD>
   <TD>Broad Institute L. loa genome project</TD>
   <TD>Broad Institute L. loa genome project</TD>
Line 200: Line 201:
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>5.056%</TD>
   <TD>2015-07-23</TD><TD ALIGN=RIGHT>5.056%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.wormbase.org/species/d_immitis 26]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=dirImm1 dirImm1]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEB1797/ Dirofilaria<BR>immitis]</TD><TD>Dog&nbsp;heartworm</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEB1797/ 26]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=dirImm1 dirImm1]</TH><TD>[http://www.wormbase.org/species/d_immitis Dirofilaria<BR>immitis]</TD><TD>Dog&nbsp;heartworm</TD>
   <TD>Sep.&nbsp;2013&nbsp;(WS240/D.&nbsp;immitis&nbsp;v2.2/dirImm1)</TD>
   <TD>Sep.&nbsp;2013&nbsp;(WS240/D.&nbsp;immitis&nbsp;v2.2/dirImm1)</TD>
   <TD>Edinburgh University D. immitis genome project</TD>
   <TD>Edinburgh University D. immitis genome project</TD>

Latest revision as of 18:11, 3 September 2015

see also

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 (version) source
version
Repeat
Masker
Window
Masker
chain
on ce11
% of ce11
matched
(chainLink table)
01ce11Caenorhabditis
elegans
C. elegans Aug. 2014 (WBcel245/ce11) Washington University School of Medicine GSC and Sanger Institute WBcel245 2015-06-10 2015-06-10 N/AN/A
02caeSp51Caenorhabditis
sp5
ju800
C. sp. 5 ju800 Jan. 2012 (WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51) University of Edinburgh Caenorhabditis sp. 5 genome project 2015-07-08 2015-07-08 2015-07-0940.332%
03caePb3Caenorhabditis
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 2015-07-0140.638%
04caeRem4Caenorhabditis
remanei
C. remanei Jul. 2007 (WS220/caeRem4) Washington University School of Medicine GSC C. remanei 15.0.1 2011-05-25 2011-05-25 2015-07-0241.715%
05cb4Caenorhabditis
briggsae
C. briggsae Apr. 2011 (WS225/cb4) Washington University School of Medicine GSC and Sanger Institute cb4 2011-05-24 2011-05-24 2015-07-0139.384%
06caeSp111Caenorhabditis
tropicalis
C. tropicalis 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 2015-07-0737.870%
07caeJap4Caenorhabditis
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 2015-06-2527.709%
08caeAng2Caenorhabditis
angaria
C. angaria Mar. 2012 (WS245/caeAng2) Division of Biology, California Institute of Technology 2015-06-30 2015-06-30 2015-06-3017.682%
09priPac3Pristionchus
pacificus
P. pacificus Aug. 2014 (P_pacificus-v2/priPac3) Max Planck Institute for Developmental Biology P. pacificus genome project 2015-07-01 2015-07-01 2015-07-016.308%
10priExs1Pristionchus
exspectatus
P. exspectatus Mar. 2014 (WS243/P_exspectatus_v1/priExs1) Max Planck Institite for Developmental Genetics 2015-07-14 2015-07-15 2015-07-236.222%
11burXyl1Bursaphelenchus
xylophilus
Pine wood nematode Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1) Wellcome Trust Sanger Institute B. xylophilus genome project 2015-07-09 2015-07-09 2015-07-096.291%
12ancCey1Ancylostoma
ceylanicum
A. ceylanicum Mar. 2014 (WS243/Acey_2013.11.30.genDNA/ancCey1) Cornell University Ancylostoma ceylanicum genome project 2015-07-15 2015-07-15 2015-07-239.736%
13haeCon2Haemonchus
contortus
Barber pole worm Jul. 2013 (WormBase WS239/haeCon2) Sanger Institute 2015-07-02 2015-07-06 2015-07-078.936%
14necAme1Necator
americanus
N. americanus Dec. 2013 (WS242/N_americanus_v1/necAme1) The Genome Institute at Washington University 2015-07-15 2015-07-15 2015-07-238.902%
15panRed1Panagrellus
redivivus
Microworm Feb. 2013 (Pred3/panRed1) California Institute of Technology P. redivivus genome project 2015-07-01 2015-07-01 2015-07-016.585%
16hetBac1Heterorhabditis
bacteriophora
H. bacteriophora/m31e Aug. 2011 (WS229/H. bacteriophora 7.0/hetBac1) Washington University Genome Sequencing Center Heterorhabditis_bacteriophora-7.0 2015-07-14 2015-07-15 2015-07-2310.486%
17ascSuu1Ascaris
suum
Pig roundworm Sep. 2012 (WS229/AscSuum_1.0/ascSuu1) Beijing Genomics Institute 2015-07-13 2015-07-14 2015-07-235.722%
18strRat2Strongyloides
ratti
Threadworm Sep. 2014 (S. ratti ED321/strRat2) Wellcome Trust Sanger Institute S. ratti genome project 2015-07-08 2015-07-08 2015-07-095.669%
19triSpi1Trichinella
spiralis
Trichinella Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1) WashU School of Medicine T. spiralis genome project 2015-07-10 2015-07-15 2015-07-232.848%
20triSui1Trichuris
suis
Whipworm Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1) University of Melboure T. suis (male) genome project 2015-07-10 2015-07-15 2015-07-232.917%
21melInc2Meloidogyne
incognita
M. incognita Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2) Sanger and Genoscope 2015-06-30 2015-06-30 2015-06-303.516%
22melHap1Meloidogyne
hapla
M. hapla Sep. 2008 (M. hapla VW9 WS210/melHap1) The Center for the Biology of Nematode Parasitism, N.C. State 2010-09-21 2010-09-21 2015-06-263.916%
23bruMal2Brugia
malayi
Filarial worm May. 2014 (WS244/B_malayi-3.1/bruMal2) University of Pittsburgh B. malayi genome project 2015-08-11 2015-08-11 2015-08-115.065%
24oncVol1Onchocerca
volvulus
O. volvulus Nov. 2013 (WS241/O_volvulus_Cameroon_v3/oncVol1) Wellcome Trust Sanger Institute O. volvulus genome project 2015-08-10 2015-08-10 2015-08-105.193%
25loaLoa1Loa
loa
Eye worm Jul. 2012 (WS235/L_loa_Cameroon_isolate/loaLoa1) Broad Institute L. loa genome project 2015-07-10 2015-07-15 2015-07-235.056%
26dirImm1Dirofilaria
immitis
Dog heartworm Sep. 2013 (WS240/D. immitis v2.2/dirImm1) Edinburgh University D. immitis genome project 2015-07-09 2015-07-09 2015-07-235.005%