Ce10 conservation alignment: Difference between revisions

Latest revision as of 15:34, 13 June 2011

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%

@@ Line 3: / Line 3: @@
 <UL>
 <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>
 </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==
@@ Line 13: / Line 29: @@
 <TABLE BORDER=1>
 <TR>
-   <TH>URL&nbsp;to<BR>assembly<BR>information</TH>
+   <TH>URL&nbsp;to<BR>assembly<BR>sequence</TH>
-   <TH>UCSC&nbsp;db&nbsp;name/<BR>genome-test<BR>browser</TH>
+   <TH>UCSC&nbsp;db&nbsp;name/<BR>genome-preview<BR>browser</TH>
-   <TD>Scientific&nbsp;name/<BR>assembly&nbsp;sequence</TD>
+   <TD>Scientific&nbsp;name/<BR>assembly&nbsp;information</TD>
    <TD>Common<BR>name</TD>
    <TD>assembly&nbsp;date</TD>
@@ Line 21: / Line 37: @@
    <TD>Repeat<BR>Masker</TD>
    <TD>Window<BR>Masker</TD>
+  <TD>chain<BR>on&nbsp;ce10</TD>
+  <TD>%&nbsp;of&nbsp;ce10<BR>matched<BR>(chainLink&nbsp;table)</TD>
 </TR>
 <TR>
-   <TH>[http://wiki.wormbase.org/index.php/Caenorhabditis_elegans 01]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ce10 ce10]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/ Caenorhabditis<BR>elegans]</TD><TD>C.&nbsp;elegans</TD>
+   <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.&nbsp;elegans</TD>
    <TD>Oct.&nbsp;2010&nbsp;(WS220/ce10)</TD>
    <TD>Washington University School of Medicine GSC and Sanger Institute WS220</TD>
    <TD ALIGN=RIGHT>2011-05-23</TD>
    <TD ALIGN=RIGHT>N/A</TD>
+  <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
 </TR><TR>
-   <TH>[http://www.sanger.ac.uk/Projects/C_briggsae/ 02]</TH><TH>[http://genome-test.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/ 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.&nbsp;briggsae</TD>
    <TD>Apr.&nbsp;2011&nbsp;(WS225/cb4)</TD>
    <TD>Washington University School of Medicine GSC and Sanger Institute cb4 </TD>
    <TD ALIGN=RIGHT>2011-05-24</TD>
    <TD ALIGN=RIGHT>2011-05-24</TD>
+  <TD>2011-06-07</TD><TD ALIGN=RIGHT>39.386%</TD>
 </TR><TR>
-   <TH>[http://genome.wustl.edu/genomes/view/caenorhabditis_remanei/ 03]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeRem4 caeRem4]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_remanei/ Caenorhabditis<BR>remanei]</TD><TD>C.&nbsp;remanei</TD>
+   <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.&nbsp;sp.&nbsp;9&nbsp;ju1422</TD>
+  <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;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 ALIGN=RIGHT>2011-05-27</TD>
+  <TD ALIGN=RIGHT>2011-05-31</TD>
+  <TD>2011-06-07</TD><TD ALIGN=RIGHT>42.169%</TD>
+</TR><TR>
+  <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.&nbsp;remanei</TD>
    <TD>Jul.&nbsp;2007&nbsp;(WS220/caeRem4)</TD>
    <TD>Washington University School of Medicine GSC C. remanei 15.0.1</TD>
    <TD ALIGN=RIGHT>2011-05-25</TD>
    <TD ALIGN=RIGHT>2011-05-25</TD>
+  <TD>2011-06-07</TD><TD ALIGN=RIGHT>41.722%</TD>
 </TR><TR>
-   <TH>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABEG02 04]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caePb3 caePb3]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_brenneri/ Caenorhabditis<BR>brenneri]</TD><TD>C.&nbsp;brenneri</TD>
+   <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.&nbsp;sp.&nbsp;11&nbsp;ju1373</TD>
-   <TD>Nov.&nbsp;2010&nbsp;(WS220/caePb3)</TD>
+   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;3.0.1/caeSp111)</TD>
-   <TD>Washington University School of Medicine GSC Caenorhabditis brenneri(PB2801) 6.0.1b</TD>
+   <TD>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186765.1)</TD>
-   <TD ALIGN=RIGHT>2011-05-26</TD>
+   <TD ALIGN=RIGHT>2011-05-31</TD>
-   <TD ALIGN=RIGHT>2011-05-26</TD>
+   <TD ALIGN=RIGHT>2011-05-31</TD>
+  <TD>2011-06-07</TD><TD ALIGN=RIGHT>37.876%</TD>
 </TR><TR>
-   <TH>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABLE03 05]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeJap4 caeJap4]</TH><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_japonica/ Caenorhabditis<BR>japonica]</TD><TD>C.&nbsp;japonica</TD>
+   <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.&nbsp;brenneri</TD>
-   <TD>Sep.&nbsp;2010&nbsp;(WS220/caeJap4)</TD>
+   <TD>Nov.&nbsp;2010&nbsp;(C.&nbsp;brenneri&nbsp;6.0.1b/caePb3)</TD>
-   <TD>Washington University School of Medicine GSC C. japonica 7.0.1</TD>
+   <TD>The Caenorhabditis brenneri Sequencing and Analysis Consortium (GCA_000143925.2)</TD>
-   <TD ALIGN=RIGHT>2011-05-26</TD>
+   <TD ALIGN=RIGHT>2011-06-08</TD>
-   <TD ALIGN=RIGHT>2011-05-26</TD>
+   <TD ALIGN=RIGHT>2011-06-08</TD>
+  <TD>2011-06-08</TD><TD ALIGN=RIGHT>40.644%</TD>
 </TR><TR>
-   <TH>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENL01 06]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp71 caeSp71]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_7_MAF_2007/Caenorhabditis_sp7_JU1286-4.0.1/ Caenorhabditis<BR>sp7.<BR>JU1286]</TD><TD>C.&nbsp;sp.&nbsp;7&nbsp;ju1286</TD>
+   <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.&nbsp;sp.&nbsp;7&nbsp;ju1286</TD>
    <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;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 ALIGN=RIGHT>2011-05-27</TD>
    <TD ALIGN=RIGHT>2011-05-27</TD>
+  <TD>2011-06-07</TD><TD ALIGN=RIGHT>40.236%</TD>
 </TR><TR>
-   <TH>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENM01 07]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp91 caeSp91]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ Caenorhabditis<BR>sp9.<BR>JU1422]</TD><TD>C.&nbsp;sp.&nbsp;9&nbsp;ju1422</TD>
+   <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.&nbsp;japonica</TD>
-   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;3.0.1/caeSp91)</TD>
+   <TD>Aug.&nbsp;2010&nbsp;(WUSTL&nbsp;7.0.1/caeJap4)</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 C. japonica 7.0.1 (GCA_000147155.1)</TD>
-   <TD ALIGN=RIGHT>2011-05-27</TD>
+   <TD ALIGN=RIGHT>2011-06-03</TD>
-   <TD ALIGN=RIGHT>2011-05-31</TD>
+   <TD ALIGN=RIGHT>2011-06-03</TD>
-</TR><TR>
+   <TD>2011-06-07</TD><TD ALIGN=RIGHT>27.737%</TD>
-   <TH>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEKS01 08]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp111 caeSp111]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ Caenorhabditis<BR>sp.<BR>11<BR>JU1373]</TD><TD>C.&nbsp;sp.&nbsp;11&nbsp;ju1373</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 ALIGN=RIGHT>2011-05-31</TD>
-  <TD ALIGN=RIGHT>2011-05-31</TD>
 </TR><TR>
-   <TH>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEHI01 09]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeAng1 caeAng1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_PS1010/ps1010rel4/ Caenorhabditis<BR>angaria]</TD><TD>C.&nbsp;angaria</TD>
+   <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.&nbsp;angaria</TD>
    <TD>Oct.&nbsp;2010&nbsp;(WS225/caeAng1)</TD>
    <TD>Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1)</TD>
    <TD ALIGN=RIGHT>2011-05-31</TD>
    <TD ALIGN=RIGHT>2011-05-31</TD>
+  <TD>2011-06-08</TD><TD ALIGN=RIGHT>17.625%</TD>
 </TR>
 </TABLE>

Ce10 conservation alignment: Difference between revisions

Latest revision as of 15:34, 13 June 2011

see also

UCSC and external download locations

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