We applied both Murasaki and the BLASTZ+TBA approach described above to the X chromosomes of eight mammals: human, mouse, rat, chimp, rhesus, orangutan, dog, and cow.
To test the scalability of Murasaki for full multiple genome comparisons, we repeated the comparison to existing methods test on eight mammals (human, mouse, rat, chimp, rhesus, orangutan, dog, and cow), however this time using the whole genome rather than just the X chromosomes.
Using the alignment, we generated a phylogenetic maximum-likelihood tree of mouse, rat, chimp and human orthologs.
Sequences of hESC-specific TF-binding sites do not intersect with any chains in the mouse, rat, chimp, gorilla, orangutan, gibbon, rhesus, and marmoset genomes.
Indeed, we have found that the orthologues of yeast HI genes are significantly under-represented on the X chromosome of the human, mouse, rat, chimp, dog, cow and horse (XY species) and the X chromosome of the nematode worm (X0) (see Table 4).
We observed the same trend by choosing 4 relatively well-studied mammals: human, mouse, rat, and chimp, and used the "all" information (without removing those peptides labeled as "novel", and including all paralogous information) provided by Ensembl to perform the same analysis.
Therefore we also analyzed our SNPs using new MCS scores derived from both "5-way" alignments of genomic sequences (human, mouse, rat, chick, and Fugu) and "8-way" species alignments (human, chimp, mouse, rat, dog, chick, Fugu, and zebrafish) (Margulies, unpublished).
The seventeen species include mouse, rat, rabbit, human, chimp, macaque, dog, cow, armadillo, elephant, tenrec, opossum, chicken, frog, zebrafish, tetraodon and fugu.
We located evolutionarily conserved regions by calculating the percent identity in all 2 kb regions spanning the Olig2 promoter using multiple alignments of seventeen species: mouse, rat, rabbit, human, chimp, macaque, dog, cow, armadillo, elephant, tenrec, opossum, chicken, frog, zebrafish, tetraodon and fugu.
Comparative sequence alignments of novel regulatory regions found in human, chimp, mouse, rat and dog were obtained from the UCSC Genome Browser (http://genome.ucsc.edu/).ucsc.edu/
Based on the multiz-8-way alignments for human, chimp, mouse, rat, dog, chicken, fugu and zebrafish [27], we generated overlaid versions of the human genome with corresponding sequences from the other seven species.
