2011年10月20日星期四

comparative genomics tools - whole genome alignments

Here you could find whole genome alignments for different genome pairs, these alignments are usually crucial for a comparative genomic study.

http://pipeline.lbl.gov/downloads.shtml

Alignments

Human - Rhesus - Horse - Dog - Mouse - Rat - Chicken 14-May-2008
Human - Orangutan - Rhesus - Marmoset 14-Dec-2007
Human - Chimp 09-Apr-2007
Human - Dog 02-Apr-2007
Human - Mouse 27-Mar-2007
Human - Dog - Mouse - Rat - Chicken 3-Dec-2006
Human (Jul. 2003) - Mouse - Rat 14-Mar-2004
Human (Apr. 2003) - Mouse - Rat 22-Aug-2003

A. thaliana Jun. 2009 (TAIR9)

Arabidopsis - Maize B73 v.2 16-Jun-2010
Arabidopsis - M. esculenta v.4 13-Jul-2010
Arabidopsis - M. guttatus v.1.0 27-Dec-2009
Arabidopsis - M. truncatula Mt3.0 25-Dec-2009
Arabidopsis - Papaya 25-Dec-2009
Arabidopsis - Poplar v.2.0 23-Dec-2009
Arabidopsis - P. patens v.1.1 07-Feb-2010
Arabidopsis - Rice v.6.0 25-Dec-2009
Arabidopsis - S. moellendorffii v.1.0 08-Feb-2010
Arabidopsis - Soybean 24-Dec-2009
Arabidopsis - Wine grape 17-Jul-2010
Arabidopsis - A. lyrata - T. halophila - C. papaya - C. clementina 11-Mar-2011

Poplar v.2.0

Poplar - Rice v.6.0 23-Dec-2009
Poplar - Papaya 26-Dec-2009

Rice v.6.0

Rice - Papaya 26-Dec-2009

A. thaliana Apr. 2008 (TAIR8)

Arabidopsis - A. lyrata 30-Jul-2008
Arabidopsis - Soybean 03-Dec-2008
Arabidopsis - Poplar v.1.1 30-Sep-2008
Arabidopsis - Medicago 18-Dec-2008
Arabidopsis - Papaya 17-Dec-2008
Arabidopsis - Wine grape 15-Aug-2008

A. thaliana Mar. 2004

Arabidopsis - Rice v.1.0 28-Jan-2005
Arabidopsis - Sorghum 04-Jan-2008
Arabidopsis - Poplar v.1.1 11-Aug-2005

Poplar v.1.1

Poplar - Arabidopsis 11-Aug-2005
Poplar - Rice v.3.0 11-Aug-2005
Poplar - Poplar 11-Aug-2005

Sorghum v.1.0

Sorghum - Arabidopsis - Rice v.5.0 22-Apr-2008
Sorghum - Sorghum 23-May-2007
Sorghum - Rice v.5.0 10-Apr-2007
Sorghum - Rice v.6.0 28-Dec-2009
Sorghum - Maize 06-Jun-2007

A. niger v.1.0

A. niger - A. fumigatus 23-Mar-2006
A. niger - A. nidulans 16-Mar-2006
A. niger - A. oryzae 23-Mar-2006

D. melanogaster Oct. 2006

D. melanogaster - D. pseudoobscura - D. yakuba - D. ananassae - D. erecta - D. simulans 13-Mar-2008

D. melanogaster Apr. 2004

D. melanogaster - D. simulans 15-July-2005
D. melanogaster - D. pseudoobscura 29-Mar-2005
D. melanogaster - D. ananassae 29-Mar-2005
D. melanogaster - D. mojavensis 29-Mar-2005
D. melanogaster - D. yakuba 29-Mar-2005
D. melanogaster - D. virilis 29-Mar-2005
D. melanogaster - D. erecta 29-Mar-2005

D. melanogaster Jan. 2003

D. melanogaster - D. pseudoobscura (LAGAN) 20-Sep-2004
D. melanogaster - D. pseudoobscura (AVID) 13-Aug-2004
D. melanogaster - D. ananassae 20-Sep-2004
D. melanogaster - D. mojavensis 20-Sep-2004
D. melanogaster - D. virilis 21-Sep-2004
D. melanogaster - D. yakuba 21-Aug-2004


Ciona intestinalis v.1.0 - Ciona savignyi 13-Aug-2004
Ciona intestinalis v.2.0 - Ciona savignyi 29-Nov-2005


Human (NCBI build 30) - Mouse (MGSCv3) (all alignments) 04-Nov-2002
Human (NCBI build 30) - Mouse (MGSCv3) (filtered alignments) 4-Nov-2002
Notes for this run


Escherichia coli O6 CFT073 25-May-2005 SLAGAN

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