For AUG2003 B1, each file contains an *.axt, *.axte, and *.axte.masked files.
The *.axt file is the original human-mouse whole-genome alignment file.
[Whole-genome human-mouse alignments (axtTight) (Schwartz et al, Human-mouse
alignments with BLASTZ. Genome Res 2003, 13:103-107 and Watertson et al,
Initial sequencing and comparative analysis of the mouse genome. Nature 2003, 420:520-562.)
between the April 2003 assembly (build 33) of the human genome and the Feb. 2003 build (mgscv4)
assembly of the mouse genome were downloaded from http://genome.ucsc.edu.]
The *.axte is the source *.axt file converted in to Emory's *.axte format and replaces repetitive
sequences with Ns.
The *.axte.masked file replaced any detected non-unique probe sequence (with N's)
found in the *.axte file.
For OCT 2003 b2, each chromosome file contains the Multiz human-mouse-rat whole genome alignments (generated by W. Miller and J. Kent, Human build15, Mouse build Feb. 2003, Rat build Jan 2003,maf format, downloaded from http://genome.ucsc.edu).
For FEB_2004_mammals_1, the alignments files listed above for both the AUG_2003_b1 and OCT_2003_b2 probes were reused as the basis for this probe set.
For MAR_2004_birds/reptiles_1, each file contains the original *.axt alignment file of chicken (galGal2) and human (build 34) downloaded from http://genome.ucsc.edu, and the corresponding *.axte file.
For APR_2005_rodents_1.1, each file contains a modified *.maf multiz multiple alignment of mouse (mm5)-rat (rn3)-human (hg17)-dog (canFam1)-chicken (galGal2) for the corresponding mouse chromosome downloaded from http://genome.ucsc.edu in which all repetitive mouse sequence was converted to lowercase.
For APR_2005_carnivores_1.1, each file contains a *.maf multiz multiple alignment of human(hg17)-chimpanzee(panTro1)-mouse(mm5)-rat(rn3)-dog(canFam1)-chicken(galGal2)-fugu(fr1)-zebra fish(danRer1) for the corresponding HUMAN chromosome downloaded from http://genome.ucsc.edu.
For JUN_2005_mammals_2, each file contains a *.maf multiz multiple alignment of human(hg17)-chimpanzee(panTro1)-mouse(mm5)-rat(rn3)-dog(canFam1)-chicken(galGal2)-fugu(fr1)-zebra fish(danRer1) for the corresponding HUMAN chromosome downloaded from http://genome.ucsc.edu.
For JUN_2005_marsupials_1, each file contains a *.axte blastz alignment of human(hg17) and opossum (monDom1) for the corresponding HUMAN chromosome downloaded from http://genome.ucsc.edu.
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