Hg18 44way alignment

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Revision as of 19:51, 17 October 2008 by Hiram (talk | contribs) (→‎sanity)
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see also

Genome size statistics

sanity

The table below needs to be examined for sanity. The "chain on hg18" date should be after 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.

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
RepeatMasker WindowMasker chain
on hg18
01 hg18 Homo
sapiens
Human Mar. 2006 NCBI Build 36.1 2005-12-09 2006-12-05 N/A
02 panTro2 Pan
troglodytes
Chimp Mar. 2006 Washington University Build 2 Version 1 2006-03-24 N/A 2006-07-15
03 gorGor1 N/A N/A N/A N/A N/A N/A N/A
04 ponAbe2 Pongo
pygmaeus
abelii
Orangutan July 2007 WUSTL 3.0 2007-09-15 N/A 2007-10-03
05 rheMac2 Macaca
mulatta
Rhesus Jan. 2006 Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4 2006-01-30 N/A 2006-03-17
06 calJac1 Callithrix
jacchus
Marmoset June 2007 WUSTL 2.0.2 2007-08-23 N/A 2007-11-13
07 tarSyr1 Tarsier
syrichta
Tarsier Aug. 2008 Broad Institute tarSyr1 2008-10-15 N/A 2008-07-28
08 otoGar1 Otolemur
garnettii
Bushbaby Dec. 2006 Broad version 1 2006-12-20 N/A 2007-02-27
09 micMur1 Microcebus
murinus
Mouse lemur Jun. 2003 Broad Institute micMur1 2008-08-03 N/A 2008-08-04
10 tupBel1 Tupaia
belangeri
TreeShrew Dec. 2006 Broad version 1 2008-10-15 N/A 2006-12-20
11 mm9 Mus
musculus
Mouse July 2007 NCBI Build 37 2007-07-20 N/A 2007-08-14
12 rn4 Rattus
norvegicus
Rat Nov. 2004 Baylor HGSC v. 3.4 2006-03-16 N/A 2006-02-17
13 dipOrd1 Dipodomys
ordii
Kangaroo rat Jul. 2008 Broad Institute 2008-10-15 N/A 2008-07-28
14 cavPor3 Cavia
porcellus
Guinea Pig Feb. 2008 Broad Institute cavPor3 2008-04-05 2008-04-08 2008-04-11
15 speTri1 Spermophilus
tridecemlineatus
Squirrel Feb. 2008 Broad Institute speTri1 2008-08-03 N/A 2008-08-05
16 oryCun1 Oryctolagus
cuniculus
Rabbit May 2005 Broad May 2005 2005-05-22 N/A 2007-04-17
17 ochPri2 Ochotona
princeps
Pika Jul. 2008 Broad Institute ochPri2 2008-07-28 N/A 2008-07-30
18 sorAra1 Sorex
araneus
Shrew June 2006 Broad Institute sorAra (Draft_v2) N/A N/A 2007-03-10
19 eriEur1 Erinaceus
europaeus
Hedgehog June 2006 Broad Institute eriEur1 (Draft_v1) N/A N/A 2007-03-11
20 felCat3 Felis
catus
Cat Mar. 2006 Broad Release 3 2006-10-16 N/A 2006-11-10
21 canFam2 Canis
lupus
familiaris
Dog May 2005 Broad Institute v. 2.0 2005-07-10 N/A 2005-12-29
22 equCab2 Equus
caballus
Horse Sep. 2007 Broad Institute EquCab2 2008-04-03 N/A 2008-04-11
23 pteVam1 Pteropus
vampyrus
Megabat Jul. 2008 Broad Institute pteVam1 2008-10-15 N/A 2008-07-13
24 myoLuc1 Myotis
lucifugus
Microbat Mar. 2006 Broad Institute myoLuc1 2008-07-29 N/A 2008-08-02
25 turTru1 Tursiops
truncatus
Dolphin Feb. 2008 Broad Institute turTru1 2008-10-15 N/A 2008-07-12
26 bosTau4 Bos
taurus
Cow Oct. 2007 Baylor Release 4.0 2008-03-10 N/A 2008-03-11
27 vicPac1 Vicugna
vicugna
Alpaca Jul. 2008 Broad Institute vicPac1 N/A N/A N/A
28 dasNov2 Dasypus
novemcinctus
Armadillo Jul. 2008 Broad Institute dasNov2 2008-10-07 N/A 2008-08-03
29 choHof1 Choloepus
hoffmanni
Sloth Jul. 2008 Broad Institute choHof1 2008-10-16 N/A 2008-08-05
30 echTel1 Echinops
telfairi
Tenrec July 2005 Broad July 2005 2005-08-04 N/A 2007-04-17
31 loxAfr2 Loxodonta
africana
Elephant Jul. 2008 Broad Institute loxAfr2 2008-10-07 N/A 2008-08-02
32 proCap1 Procavia
capensis
Rock hyrax Jul. 2008 Broad Institute proCap1 2008-10-16 N/A 2008-08-01
33 monDom4 Monodelphis
domestica
Opossum Jan. 2006 Broad Inst. monDom4 Jan06 2006-02-10 N/A 2006-02-13
34 ornAna1 Ornithorhynchus
anatinus
Platypus Mar. 2007 WUSTL version 5.0.1 2007-07-20 N/A 2007-04-04
35 galGal3 Gallus
gallus
Chicken May 2006 Chicken Genome Sequencing Consortium May 2006 release 2006-05-18 2007-01-02 2006-05-23
36 taeGut1 Taeniopygia
guttata
Zebra finch Jul. 2008 Washington University taeGut1 N/A 2008-08-05 2008-09-09
37 anoCar1 Anolis
carolinensis
Lizard Feb. 2007 Broad Institute AnoCar (1.0) 2007-03-07 2007-02-16 2007-02-18
38 xenTro2 Xenopus
tropicalis
X. tropicalis Aug. 2005 JGI v4.1 2006-04-17 2007-02-20 2006-04-20
39 danRer5 Danio
rerio
Zebrafish July 2007 Wellcome Trust Sanger Institute, Zv7 assembly 2007-09-05 N/A 2007-10-17
40 tetNig1 Tetraodon
nigroviridis
Tetraodon Feb. 2004 Genoscope and Broad Institute, V7 2004-08-17 2006-12-05 2006-01-07
41 fr2 Takifugu
rubripes
Fugu Oct. 2004 JGI V4.0 2007-03-07 2007-01-22 2007-01-24
42 gasAcu1 Gasterosteus
aculeatus
Stickleback Feb. 2006 Broad Institute gasAcu1 (1.0) 2006-10-17 2006-12-05 2007-02-08
43 oryLat2 Oryzias
latipes
Medaka Oct. 2005 MEDAKA1 2008-08-12 2008-08-14 2008-08-19
44 petMar1 Petromyzon
marinus
Lamprey Mar. 2007 WUSTL v.3.0 (March 2007) N/A 2008-01-28 2008-01-29