The alignments in this track were generated using PECAN, a consistency-based multiple aligner. The conservation subtracks display conservation scores and conserved elements generated by GERP. GERP scores each column of the alignment by quantifying rejected substitutions. These scores are then used to find regions of the alignment where high scores accumulate.
The multiple alignments are based on a set of 9-way EPO (Enredo-Pecan-Ortheus) alignments for all high-coverage placental mammal genomes. 22 low coverage genomes (including guinea pig) were mapped onto the alignments using the BlastZ-net alignments to the human genome. Insertions in the low coverage genomes are ignored, i.e. low-coverage genome-specific sequence is removed from the alignments.
The multiple alignments are based on whole-genome assemblies residing at UCSC for high coverage genomes and Ensembl assemblies for low-coverage genomes. Ensembl adds an extra layer to the assembly in order to accommodate gene models. The species are:
Organism Species Version Human Homo sapiens UCSC hg18 Chimpanzee Pan troglodytes UCSC panTro2 Orangutan Pongo abelii UCSC ponAbe2 Macaque Macaca mulatta UCSC rheMac2 Mouse Mus musculus UCSC mm9 Rat Rattus norvegicus UCSC rn4 Dog Canis familiaris UCSC canFam2 Cow Bos taurus UCSC bosTau3 Horse Equus caballus UCSC equCab2 Guinea pig Cavia porcellus Ensembl Sloth Choloepus hoffmanni Ensembl Armadillo Dasypus novemcinctus Ensembl Kangaroo rat Dipodomys ordii Ensembl Tenrec Echinops telfairi Ensembl European Hedgehog Erinaceus europaeus Ensembl Cat Felis catus Ensembl Gorilla Gorilla gorilla Ensembl Elephant Loxodonta africana Ensembl Mouse Lemur Microcebus murinus Ensembl Bat (sbbat) Myotis lucifugus Ensembl Pika Ochotona princeps Ensembl Rabbit Oryctolagus cuniculus Ensembl Galago Otolemur garnettii Ensembl Rock hyrax Procavia capensis Ensembl Flying Fox Pteropus vampyrus Ensembl Shrew Sorex araneus Ensembl Squirrel Spermophilus tridecemlineatus Ensembl Tarsier Tarsius syrichta Ensembl Tree shrew Tupaia belangeri Ensembl Dolphin Tursiops truncatus Ensembl Alpaca Vicugna pacos Ensembl
We used GERP v2.1b to score each column of the alignment. This is done by comparing the number expected with the number of observed substitutions in every column of the alignment. These scores are then used to find regions of the alignment whith more high conservation scores than expected by chance.
The PECAN multiple alignments were created by Kathryn Beal, Stephen Fitzgerald and Javier Herrero from the Ensembl team.
ENREDO was developed by Javier Herrero (Paten et al. 2008).
PECAN was developed by Benedict Paten (Paten et al. 2008).
GERP 2.1b was written by Eugene Davydov (Cooper et al. 2005).
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res. 2008 Nov;18(11):1814-28.
Cooper G, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, and Sidow A. Distribution and intensity of constraint in mammalian genomic sequence Genome Res. 2005 Jul;15(7):901-13.