Hg18 44way alignment: Difference between revisions

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<UL>
<UL>
<LI>[[Genome size statistics]]</LI>
<LI>Human 44-way [[Genome size statistics|Hg18 Genome size statistics]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>Human 44-way [[Hg18 44way blastz parameters|Hg18 conservation lastz parameters]]</LI>
<LI>[[Hg19 Genome size statistics]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>[[Hg19 conservation lastz parameters]]</LI>
</UL>
</UL>
==sanity==
The table below needs to be examined for sanity.  The "chain on hg18" date should be <em>after</em> the masking date.  Some of these existing pair-wise alignments need to be re-done since the genomes have been properly repeat masked.  When all the chain tables exist, that is a good sign that the multiple alignment can be done.


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</TR>
</TR>
</TABLE>
</TABLE>
[[Category:Comparative Genomics]]

Latest revision as of 22:42, 18 May 2011

see also

do not edit

This table is automatically generated off-line from the UCSC databases. Please do not edit it.

  UCSC
db name		 Scientific
name		 Common
name		 assembly
date		 source
version		 Repeat
Masker		 Window
Masker		 chain
on hg18		 % of hg18
matched
(chainLink table)
01hg18Homo
sapiens		Human Mar. 2006NCBI Build 36.12005-12-09 2006-12-05N/AN/A
02panTro2Pan
troglodytes		Chimp Mar. 2006Washington University Build 2 Version 12006-03-24 N/A2006-07-1594.888%
03gorGor1Gorilla
gorilla
gorilla		Gorilla Oct. 2008Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000)2008-11-03 N/A2008-11-0561.731%
04ponAbe2Pongo
pygmaeus
abelii		Orangutan July 2007WUSTL 3.02007-09-15 N/A2007-10-0392.892%
05rheMac2Macaca
mulatta		Rhesus Jan. 2006Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit42006-01-30 N/A2006-03-1785.552%
06calJac1Callithrix
jacchus		Marmoset June 2007WUSTL 2.0.22007-08-23 N/A2007-11-1378.351%
07tarSyr1Tarsier
syrichta		Tarsier Aug. 2008Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000)2008-10-15 N/A2008-10-2747.999%
08otoGar1Otolemur
garnettii		Bushbaby Dec. 2006Broad version 1 (NCBI project 16955, AAQR00000000)2006-12-20 N/A2007-02-2744.638%
09micMur1Microcebus
murinus		Mouse lemur Jun. 2003Broad Institute micMur1 (NCBI project 19967, ABDC00000000)2008-08-03 N/A2008-08-0446.445%
10tupBel1Tupaia
belangeri		TreeShrew Dec. 2006Broad Institute tupBel1 (NCBI project 13971, AAPY01000000)2008-10-15 N/A2006-12-2037.348%
11mm9Mus
musculus		Mouse July 2007NCBI Build 372007-07-20 N/A2007-08-1435.201%
12rn4Rattus
norvegicus		Rat Nov. 2004Baylor HGSC v. 3.42006-03-16 N/A2006-02-1732.893%
13dipOrd1Dipodomys
ordii		Kangaroo rat Jul. 2008Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000)2008-10-15 N/A2008-10-2227.282%
14cavPor3Cavia
porcellus		Guinea Pig Feb. 2008Broad Institute cavPor32008-04-05 2008-04-082008-04-1143.971%
15speTri1Spermophilus
tridecemlineatus		Squirrel Feb. 2008Broad Institute speTri12008-08-03 N/A2008-08-0535.828%
16oryCun1Oryctolagus
cuniculus		Rabbit May 2005Broad May 20052005-05-22 N/A2007-04-1734.015%
17ochPri2Ochotona
princeps		Pika Jul. 2008Broad Institute ochPri22008-07-28 N/A2008-07-3027.974%
18sorAra1Sorex
araneus		Shrew June 2006Broad Institute sorAra1 (Draft_v2)2008-10-20 2008-10-212007-03-1020.056%
19eriEur1Erinaceus
europaeus		hedgehog June 2006Broad Institute eriEur1 (Draft_v1)2008-10-21 2008-10-212007-03-1119.622%
20felCat3Felis
catus		Cat Mar. 2006Broad Release 32006-10-16 N/A2006-11-1035.888%
21canFam2Canis
lupus
familiaris		Dog May 2005Broad Institute v. 2.02005-07-10 N/A2005-12-2952.915%
22equCab2Equus
caballus		Horse Sep. 2007Broad Institute EquCab22008-04-03 N/A2008-04-1157.162%
23pteVam1Pteropus
vampyrus		Megabat Jul. 2008Broad Institute pteVam1 (NCBI project 20325, ABRP01000000)2008-10-15 N/A2008-10-2245.502%
24myoLuc1Myotis
lucifugus		Microbat Mar. 2006Broad Institute myoLuc12008-07-29 N/A2008-08-0233.044%
25turTru1Tursiops
truncatus		Dolphin Feb. 2008Broad Institute turTru1 (NCBI project 20367, ABRN01000000)2008-10-15 N/A2008-10-2248.537%
26bosTau4Bos
taurus		Cow Oct. 2007Baylor Release 4.02008-03-10 N/A2008-03-1146.689%
27vicPac1Vicugna
pacos		Alpaca Jul. 2008Broad Institute vicPac12008-10-17 N/A2008-10-2839.531%
28dasNov2Dasypus
novemcinctus		Armadillo Jul. 2008Broad Institute dasNov2 (NCBI project 12594, AAGV020000000)2008-10-07 N/A2008-10-2733.663%
29choHof1Choloepus
hoffmanni		Sloth Jul. 2008Broad Institute choHof12008-10-16 N/A2008-10-2434.463%
30echTel1Echinops
telfairi		Tenrec July 2005Broad July 20052005-08-04 N/A2007-04-1723.645%
31loxAfr2Loxodonta
africana		Elephant Jul. 2008Broad Institute loxAfr2 (NCBI project 12569, AAGU02000000)2008-10-07 N/A2008-10-2735.204%
32proCap1Procavia
capensis		Rock hyrax Jul. 2008Broad Institute proCap1 (NCBI project 13972, ABRQ01000000)2008-10-16 N/A2008-10-2430.935%
33monDom4Monodelphis
domestica		Opossum Jan. 2006Broad Inst. monDom4 Jan062006-02-10 N/A2006-02-1312.385%
34ornAna1Ornithorhynchus
anatinus		Platypus Mar. 2007WUSTL version 5.0.12007-07-20 N/A2007-04-047.870%
35galGal3Gallus
gallus		Chicken May 2006Chicken Genome Sequencing Consortium May 2006 release2006-05-18 2007-01-022006-05-233.589%
36taeGut1Taeniopygia
guttata		Zebra finch Jul. 2008Washington University taeGut1N/A 2008-08-052008-09-093.503%
37anoCar1Anolis
carolinensis		Lizard Feb. 2007Broad Institute AnoCar (1.0)2007-03-07 2007-02-162007-02-184.774%
38xenTro2Xenopus
tropicalis		X. tropicalis Aug. 2005JGI v4.12006-04-17 2007-02-202006-04-202.623%
39danRer5Danio
rerio		Zebrafish July 2007Wellcome Trust Sanger Institute, Zv7 assembly2007-09-05 N/A2007-10-172.565%
40tetNig1Tetraodon
nigroviridis		Tetraodon Feb. 2004Genoscope and Broad Institute V7 (NCBI project 12350, CAAE01000000)2004-08-17 2006-12-052006-01-072.001%
41fr2Takifugu
rubripes		Fugu Oct. 2004JGI V4.02007-03-07 2007-01-222007-01-241.766%
42gasAcu1Gasterosteus
aculeatus		Stickleback Feb. 2006Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000)2006-10-17 2006-12-052007-02-081.923%
43oryLat2Oryzias
latipes		Medaka Oct. 2005NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000)2008-08-12 2008-08-142008-08-191.829%
44petMar1Petromyzon
marinus		Lamprey Mar. 2007WUSTL v.3.0 (March 2007)N/A 2008-01-282008-01-291.251%
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