Ce10 conservation alignment: Difference between revisions
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<TR><TH>UCSC download locations</TH><TH>external source locations</TH></TR> | <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/WS220/genomes/c_elegans/ WormBase WS220]</TD></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/WS220/genomes/c_briggsae/ WormBase WS225]</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/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/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/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/WS220/genomes/c_remanei/ WormBase WS220]</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/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/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> | ||
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% |
