Ce10 conservation alignment: Difference between revisions

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(indicate external source locations)
(indicate naming situation)
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<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>
<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>
</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.


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Revision as of 15:20, 13 June 2011

see also

UCSC and external download locations

UCSC download locationsexternal source locations
elegansWormBase WS220
briggsaeWormBase WS225
brenneriGenbank 6.0.1b
japonicaGenbank 7.0.1
angariaGenbank ps1010rel4
remaneiWormBase WS220
C. sp. 7 JU1286Genbank 4.0.1
C. sp. 9 JU1422Genbank 3.0.1
C. sp. 11 JU1373Genbank 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)
01ce10Caenorhabditis
elegans
C. elegans Oct. 2010 (WS220/ce10) Washington University School of Medicine GSC and Sanger Institute WS220 2011-05-23 N/A N/AN/A
02cb4Caenorhabditis
briggsae
C. briggsae Apr. 2011 (WS225/cb4) Washington University School of Medicine GSC and Sanger Institute cb4 2011-05-24 2011-05-24 2011-06-0739.386%
03caeSp91Caenorhabditis
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 2011-06-0742.169%
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 2011-06-0741.722%
05caeSp111Caenorhabditis
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 2011-06-0737.876%
06caePb3Caenorhabditis
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 2011-06-0840.644%
07caeSp71Caenorhabditis
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 2011-06-0740.236%
08caeJap4Caenorhabditis
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 2011-06-0727.737%
09caeAng1Caenorhabditis
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 2011-06-0817.625%