Hg18 44way alignment
From genomewiki
Jump to navigationJump to search
see also
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 |
Repeat Masker |
Window Masker |
chain on hg18 |
% of hg18 matched (chainLink table) |
|
|---|---|---|---|---|---|---|---|---|---|
| 01 | hg18 | Homo sapiens | Human | Mar. 2006 | NCBI Build 36.1 | 2005-12-09 | 2006-12-05 | N/A | N/A |
| 02 | panTro2 | Pan troglodytes | Chimp | Mar. 2006 | Washington University Build 2 Version 1 | 2006-03-24 | N/A | 2006-07-15 | 94.888% |
| 03 | gorGor1 | Gorilla gorilla gorilla | Gorilla | Oct. 2008 | Sanger Institute genome_31265 | 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 | 92.892% |
| 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 | 85.552% |
| 06 | calJac1 | Callithrix jacchus | Marmoset | June 2007 | WUSTL 2.0.2 | 2007-08-23 | N/A | 2007-11-13 | 78.351% |
| 07 | tarSyr1 | Tarsier syrichta | Tarsier | Aug. 2008 | Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000) | 2008-10-15 | N/A | 2008-10-27 | 47.999% |
| 08 | otoGar1 | Otolemur garnettii | Bushbaby | Dec. 2006 | Broad version 1 (NCBI project 16955, AAQR00000000) | 2006-12-20 | N/A | 2007-02-27 | 44.638% |
| 09 | micMur1 | Microcebus murinus | Mouse lemur | Jun. 2003 | Broad Institute micMur1 (NCBI project 19967, ABDC00000000) | 2008-08-03 | N/A | 2008-08-04 | 46.445% |
| 10 | tupBel1 | Tupaia belangeri | TreeShrew | Dec. 2006 | Broad Institute tupBel1 (NCBI project 13971, AAPY01000000) | 2008-10-15 | N/A | 2006-12-20 | 37.348% |
| 11 | mm9 | Mus musculus | Mouse | July 2007 | NCBI Build 37 | 2007-07-20 | N/A | 2007-08-14 | 35.201% |
| 12 | rn4 | Rattus norvegicus | Rat | Nov. 2004 | Baylor HGSC v. 3.4 | 2006-03-16 | N/A | 2006-02-17 | 32.893% |
| 13 | dipOrd1 | Dipodomys ordii | Kangaroo rat | Jul. 2008 | Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000) | 2008-10-15 | N/A | 2008-10-22 | 27.282% |
| 14 | cavPor3 | Cavia porcellus | Guinea Pig | Feb. 2008 | Broad Institute cavPor3 | 2008-04-05 | 2008-04-08 | 2008-04-11 | 43.971% |
| 15 | speTri1 | Spermophilus tridecemlineatus | Squirrel | Feb. 2008 | Broad Institute speTri1 | 2008-08-03 | N/A | 2008-08-05 | 35.828% |
| 16 | oryCun1 | Oryctolagus cuniculus | Rabbit | May 2005 | Broad May 2005 | 2005-05-22 | N/A | 2007-04-17 | 34.015% |
| 17 | ochPri2 | Ochotona princeps | Pika | Jul. 2008 | Broad Institute ochPri2 | 2008-07-28 | N/A | 2008-07-30 | 27.974% |
| 18 | sorAra1 | Sorex araneus | Shrew | June 2006 | Broad Institute sorAra1 (Draft_v2) | 2008-10-20 | 2008-10-21 | 2007-03-10 | 20.056% |
| 19 | eriEur1 | Erinaceus europaeus | hedgehog | June 2006 | Broad Institute eriEur1 (Draft_v1) | 2008-10-21 | 2008-10-21 | 2007-03-11 | 19.622% |
| 20 | felCat3 | Felis catus | Cat | Mar. 2006 | Broad Release 3 | 2006-10-16 | N/A | 2006-11-10 | 35.888% |
| 21 | canFam2 | Canis lupus familiaris | Dog | May 2005 | Broad Institute v. 2.0 | 2005-07-10 | N/A | 2005-12-29 | 52.915% |
| 22 | equCab2 | Equus caballus | Horse | Sep. 2007 | Broad Institute EquCab2 | 2008-04-03 | N/A | 2008-04-11 | 57.162% |
| 23 | pteVam1 | Pteropus vampyrus | Megabat | Jul. 2008 | Broad Institute pteVam1 (NCBI project 20325, ABRP01000000) | 2008-10-15 | N/A | 2008-10-22 | 45.502% |
| 24 | myoLuc1 | Myotis lucifugus | Microbat | Mar. 2006 | Broad Institute myoLuc1 | 2008-07-29 | N/A | 2008-08-02 | 33.044% |
| 25 | turTru1 | Tursiops truncatus | Dolphin | Feb. 2008 | Broad Institute turTru1 (NCBI project 20367, ABRN01000000) | 2008-10-15 | N/A | 2008-10-22 | 48.537% |
| 26 | bosTau4 | Bos taurus | Cow | Oct. 2007 | Baylor Release 4.0 | 2008-03-10 | N/A | 2008-03-11 | 46.689% |
| 27 | vicPac1 | Vicugna pacos | Alpaca | Jul. 2008 | Broad Institute vicPac1 | 2008-10-17 | N/A | 2008-10-28 | 39.531% |
| 28 | dasNov2 | Dasypus novemcinctus | Armadillo | Jul. 2008 | Broad Institute dasNov2 (NCBI project 12594, AAGV020000000) | 2008-10-07 | N/A | 2008-10-27 | 33.663% |
| 29 | choHof1 | Choloepus hoffmanni | Sloth | Jul. 2008 | Broad Institute choHof1 | 2008-10-16 | N/A | 2008-10-24 | 34.463% |
| 30 | echTel1 | Echinops telfairi | Tenrec | July 2005 | Broad July 2005 | 2005-08-04 | N/A | 2007-04-17 | 23.645% |
| 31 | loxAfr2 | Loxodonta africana | Elephant | Jul. 2008 | Broad Institute loxAfr2 (NCBI project 12569, AAGU02000000) | 2008-10-07 | N/A | 2008-10-27 | 35.204% |
| 32 | proCap1 | Procavia capensis | Rock hyrax | Jul. 2008 | Broad Institute proCap1 (NCBI project 13972, ABRQ01000000) | 2008-10-16 | N/A | 2008-10-24 | 30.935% |
| 33 | monDom4 | Monodelphis domestica | Opossum | Jan. 2006 | Broad Inst. monDom4 Jan06 | 2006-02-10 | N/A | 2006-02-13 | 12.385% |
| 34 | ornAna1 | Ornithorhynchus anatinus | Platypus | Mar. 2007 | WUSTL version 5.0.1 | 2007-07-20 | N/A | 2007-04-04 | 7.870% |
| 35 | galGal3 | Gallus gallus | Chicken | May 2006 | Chicken Genome Sequencing Consortium May 2006 release | 2006-05-18 | 2007-01-02 | 2006-05-23 | 3.589% |
| 36 | taeGut1 | Taeniopygia guttata | Zebra finch | Jul. 2008 | Washington University taeGut1 | N/A | 2008-08-05 | 2008-09-09 | 3.503% |
| 37 | anoCar1 | Anolis carolinensis | Lizard | Feb. 2007 | Broad Institute AnoCar (1.0) | 2007-03-07 | 2007-02-16 | 2007-02-18 | 4.774% |
| 38 | xenTro2 | Xenopus tropicalis | X. tropicalis | Aug. 2005 | JGI v4.1 | 2006-04-17 | 2007-02-20 | 2006-04-20 | 2.623% |
| 39 | danRer5 | Danio rerio | Zebrafish | July 2007 | Wellcome Trust Sanger Institute, Zv7 assembly | 2007-09-05 | N/A | 2007-10-17 | 2.565% |
| 40 | tetNig1 | Tetraodon nigroviridis | Tetraodon | Feb. 2004 | Genoscope and Broad Institute V7 (NCBI project 12350, CAAE01000000) | 2004-08-17 | 2006-12-05 | 2006-01-07 | 2.001% |
| 41 | fr2 | Takifugu rubripes | Fugu | Oct. 2004 | JGI V4.0 | 2007-03-07 | 2007-01-22 | 2007-01-24 | 1.766% |
| 42 | gasAcu1 | Gasterosteus aculeatus | Stickleback | Feb. 2006 | Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000) | 2006-10-17 | 2006-12-05 | 2007-02-08 | 1.923% |
| 43 | oryLat2 | Oryzias latipes | Medaka | Oct. 2005 | NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000) | 2008-08-12 | 2008-08-14 | 2008-08-19 | 1.829% |
| 44 | petMar1 | Petromyzon marinus | Lamprey | Mar. 2007 | WUSTL v.3.0 (March 2007) | N/A | 2008-01-28 | 2008-01-29 | 1.251% |
