In MULTIPIPMAKER, the reference mouse sequences were compared with the corresponding human, chimp, rat and dog genomic sequences in order to identify regions of high conservation across species.
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/
Five species analyzed (human, chimp, mouse, rat and dog) were obtained from Ensembl release 48 [ 31].
To check if target site conservation is a considerable factor in predicting siRNA off-targets, we searched for sites conserved among human, chimp, mouse, rat and dog.
A region of mouse chromosome 13 (and of chimp chromosome 6 and dog chromosome 35, data not shown) showed the order and intergenic distance of these genes to be comparable in these mammals.
Genomic regions (within human genome) conserved within human, chimp, mouse, rat, and dog are then extracted and mapped within the coordinates of human mRNAs (downloaded from UCSC genome browser) to get the location of the conserved regions within human mRNAs.
We used the Biomart database to access probe specific non-synonymous (dn) to and synonymous (ds) substitution rates between humans, chimps, mice and dogs.
Sequence conservation is depicted in the form of a multiple sequence alignment of the corresponding genomic sequences of chimp, mouse, rat, cow and dog generated using the MultiZ track.
A large scale study of >16,000 human genes found around 2.4% of genes to be evolving under positive selection [75] in six mammalian genomes (human, chimp, macaque, mouse, rat and dog), which is significantly lower than 8% (binomial test, P = 0.03) identified in this study.
Apparently, no one has spent extended time near grizzlies in their shrinking natural habitats as the late Dian Fossey did with gorillas, for example, and Jane Goodall did with chimps and wild dogs.
