Multiple genome alignments
Multiple alignments are calculated between groups of genomes. These are used to calculate ancestral sequences, age of base, conservation scores and constrained elements.
Alignments available
| Name | Genomes | Method used |
|---|---|---|
| 63 amniota vertebrates | Algerian mouse, Alpine marmot, Arabian camel, Argentine black and white tegu, Australian saltwater crocodile, Beluga whale, Blue whale, Bonobo, Cat, Chacoan peccary, Chicken, Chimpanzee, Chinese hamster CHOK1GS, Common canary, Common wall lizard, Crab-eating macaque, Dingo, Dog, Domestic yak, Duck, Eastern brown snake, Elephant, Eurasian red squirrel, Gibbon, Goat, Golden eagle, Goodes thornscrub tortoise, Gorilla, Great Tit, Greater horseshoe bat, Green anole, Guinea Pig, Horse, Human, Hybrid - Bos Indicus, Indian cobra, Japanese quail, Kakapo, Leopard, Lion, Macaque, Mouse, Mouse Lemur, Narwhal, Northern American deer mouse, Olive baboon, Opossum, Pig, Platypus, Prairie vole, Rabbit, Rat, Ryukyu mouse, Shrew mouse, Sperm whale, Sumatran orangutan, Three-toed box turtle, Turkey, Vaquita, Vervet-AGM, White-tufted-ear marmoset, Yarkand deer, Zebra finch | Mercator-Pecan |
| 21 murinae | Algerian mouse, Mouse, Mouse 129S1/SvImJ, Mouse A/J, Mouse AKR/J, Mouse BALB/cJ, Mouse C3H/HeJ, Mouse C57BL/6NJ, Mouse CAST/EiJ, Mouse CBA/J, Mouse DBA/2J, Mouse FVB/NJ, Mouse LP/J, Mouse NOD/ShiLtJ, Mouse NZO/HlLtJ, Mouse PWK/PhJ, Mouse WSB/EiJ, Rat, Ryukyu mouse, Shrew mouse, Steppe mouse | EPO |
| 10 primates | Bonobo, Chimpanzee, Crab-eating macaque, Gibbon, Gorilla, Human, Macaque, Mouse Lemur, Sumatran orangutan, Vervet-AGM | EPO |
| 17 sauropsids | Argentine black and white tegu, Australian saltwater crocodile, Chicken, Common canary, Common wall lizard, Duck, Eastern brown snake, Golden eagle, Goodes thornscrub tortoise, Great Tit, Green anole, Indian cobra, Japanese quail, Kakapo, Three-toed box turtle, Turkey, Zebra finch | EPO |
| 43 eutherian mammals | Algerian mouse, Alpine marmot, Arabian camel, Beluga whale, Blue whale, Bonobo, Cat, Chacoan peccary, Chimpanzee, Chinese hamster CHOK1GS, Cow, Crab-eating macaque, Dingo, Dog, Domestic yak, Elephant, Eurasian red squirrel, Gibbon, Goat, Gorilla, Greater horseshoe bat, Guinea Pig, Horse, Human, Hybrid - Bos Indicus, Leopard, Lion, Macaque, Mouse, Mouse Lemur, Narwhal, Northern American deer mouse, Pig, Prairie vole, Rabbit, Rat, Ryukyu mouse, Sheep, Shrew mouse, Sperm whale, Vaquita, Vervet-AGM, Yarkand deer | EPO |
| 32 fish | Asian bonytongue, Atlantic salmon, Brown trout, Channel bull blenny, Coho salmon, Common carp, European seabass, Fugu, Gilthead seabream, Goldfish, Greater amberjack, Guppy, Indian medaka, Japanese medaka HdrR, Javanese ricefish, Large yellow croaker, Lumpfish, Mexican tetra, Nile tilapia, Orange clownfish, Pinecone soldierfish, Platyfish, Rainbow trout, Reedfish, Siamese fighting fish, Spotted gar, Tetraodon, Tongue sole, Turbot, Turquoise killifish, Zebra mbuna, Zebrafish | EPO |
| 27 sauropsids | Abingdon island giant tortoise, African ostrich, Argentine black and white tegu, Australian saltwater crocodile, Blue-ringed sea krait, Chicken, Chinese softshell turtle, Collared flycatcher, Common canary, Common wall lizard, Duck, Eastern brown snake, Golden eagle, Goodes thornscrub tortoise, Great Tit, Green anole, Indian cobra, Japanese quail, Kakapo, Mainland tiger snake, Medium ground-finch, Painted turtle, Pink-footed goose, Three-toed box turtle, Tuatara, Turkey, Zebra finch | EPO-Extended |
| 24 primates | Black snub-nosed monkey, Bolivian squirrel monkey, Bonobo, Bushbaby, Chimpanzee, Coquerel's sifaka, Crab-eating macaque, Drill, Gibbon, Golden snub-nosed monkey, Gorilla, Greater bamboo lemur, Human, Ma's night monkey, Macaque, Mouse Lemur, Olive baboon, Panamanian white-faced capuchin, Pig-tailed macaque, Sooty mangabey, Sumatran orangutan, Tarsier, Vervet-AGM, White-tufted-ear marmoset | EPO-Extended |
| 91 eutherian mammals | Algerian mouse, Alpaca, Alpine marmot, American bison, American black bear, American mink, Arabian camel, Arctic ground squirrel, Armadillo, Beluga whale, Black snub-nosed monkey, Blue whale, Bolivian squirrel monkey, Bonobo, Bushbaby, Cat, Chacoan peccary, Chimpanzee, Chinese hamster CHOK1GS, Coquerel's sifaka, Cow, Crab-eating macaque, Degu, Dingo, Dog, Dolphin, Domestic yak, Donkey, Drill, Elephant, Eurasian red squirrel, Ferret, Giant panda, Gibbon, Goat, Golden Hamster, Golden snub-nosed monkey, Gorilla, Greater bamboo lemur, Greater horseshoe bat, Guinea Pig, Hedgehog, Horse, Human, Hybrid - Bos Indicus, Hyrax, Kangaroo rat, Leopard, Lesser Egyptian jerboa, Lesser hedgehog tenrec, Lion, Long-tailed chinchilla, Ma's night monkey, Macaque, Megabat, Microbat, Mouse, Mouse Lemur, Naked mole-rat female, Narwhal, Northern American deer mouse, Olive baboon, Panamanian white-faced capuchin, Pig, Pig-tailed macaque, Pika, Polar bear, Prairie vole, Rabbit, Rat, Red fox, Ryukyu mouse, Sheep, Shrew, Shrew mouse, Siberian musk deer, Sloth, Sooty mangabey, Sperm whale, Squirrel, Steppe mouse, Sumatran orangutan, Tarsier, Tiger, Tree Shrew, Upper Galilee mountains blind mole rat, Vaquita, Vervet-AGM, White-tufted-ear marmoset, Wild yak, Yarkand deer | EPO-Extended |
| 65 fish | Amazon molly, Asian bonytongue, Atlantic cod, Atlantic herring , Atlantic salmon, Ballan wrasse, Barramundi perch, Bicolor damselfish, Brown trout, Burton's mouthbrooder, Channel bull blenny, Channel catfish, Chinese medaka, Chinook salmon, Climbing perch, Clown anemonefish, Coho salmon, Common carp, Denticle herring, Eastern happy, Electric eel, European seabass, Fugu, Gilthead seabream, Golden-line barbel, Goldfish, Greater amberjack, Guppy, Huchen, Indian medaka, Japanese medaka HdrR, Javanese ricefish, Large yellow croaker, Lumpfish, Lyretail cichlid, Makobe Island cichlid, Mangrove rivulus, Mexican tetra, Midas cichlid, Mummichog, Nile tilapia, Northern pike, Orange clownfish, Paramormyrops kingsleyae, Pike-perch, Pinecone soldierfish, Platyfish, Rainbow trout, Red-bellied piranha, Reedfish, Sailfin molly, Sheepshead minnow, Siamese fighting fish, Spiny chromis, Spotted gar, Stickleback, Tetraodon, Tiger tail seahorse, Tongue sole, Turbot, Turquoise killifish, Yellowtail amberjack, Zebra mbuna, Zebrafish, Zig-zag eel | EPO-Extended |
| 23 pig breeds | Cow, Horse, Pig, Pig - Bama miniature, Pig - Bamei, Pig - Berkshire, Pig - Duroc, Pig - Hampshire, Pig - Jinhua, Pig - Landrace, Pig - Largewhite, Pig - Meishan, Pig - NIHS-2020, Pig - Ningxiang, Pig - Ossabaw miniature, Pig - PB115, Pig - Pietrain, Pig - Rongchang, Pig - Tibetan, Pig - Wuzhishan, Pig - euw1 (european wild boar), Pig USMARC, Sheep | EPO-Extended |
| 10 fowl | Chicken, Chicken (Red Jungle fowl), Chicken (paternal White leghorn layer), Helmeted guineafowl, Indian peafowl, Japanese quail, Mallard, Muscovy Duck (domestic type), Pink-footed goose, Ring-necked pheasant | Cactus |
| 31 primates | Angola colobus, Black snub-nosed monkey, Bolivian squirrel monkey, Bonobo, Bushbaby, Chicken, Chimpanzee, Coquerel's sifaka, Crab-eating macaque, Drill, Gelada, Gibbon, Golden snub-nosed monkey, Gorilla, Greater bamboo lemur, Green anole, Human, Ma's night monkey, Macaque, Mouse, Mouse Lemur, Olive baboon, Panamanian white-faced capuchin, Pig-tailed macaque, Sooty mangabey, Sumatran orangutan, Tarsier, Tropical clawed frog, Ugandan red Colobus, Vervet-AGM, White-tufted-ear marmoset | Cactus |
| 27 rodents | Alpine marmot, American beaver, Arctic ground squirrel, Brazilian guinea pig, Chicken, Chinese hamster PICR, Damara mole rat, Daurian ground squirrel, Degu, Eurasian red squirrel, Golden Hamster, Green anole, Guinea Pig, Human, Kangaroo rat, Lesser Egyptian jerboa, Long-tailed chinchilla, Mongolian gerbil, Mouse, Naked mole-rat female, Northern American deer mouse, Prairie vole, Rat, Squirrel, Steppe mouse, Tropical clawed frog, Upper Galilee mountains blind mole rat | Cactus |
Alignment methods
PECAN Multiple Alignment
Pecan is used to provide global multiple genomic alignments. First, Mercator is used to build a synteny map between the genomes and then Pecan builds alignments in these syntenic regions.
Pecan is a global multiple sequence alignment program that makes practical the probabilistic consistency methodology for significant numbers of sequences of practically arbitrary length. As input it takes a set of sequences and a phylogenetic tree. The parameters and heuristics it employs are highly user configurable, it is written entirely in Java and also requires the installation of Exonerate.
EPO Multiple Alignment
The EPO (Enredo, Pecan, Ortheus) pipeline is a three step pipeline for whole-genome multiple alignments.
- Enredo produces colinear segments from extant genomes handling both rearrangements, deletions and duplications.
- Pecan, as described above, is used to align these segments.
- Finally, Ortheus is used to create genome-wide ancestral sequence reconstructions.
The pipeline requires alignments of so-called anchor sequences, which are explained here. Further details on all these methods can be found at: Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
EPO-Extended Multiple Alignment
Due to difficulties with running Ortheus on the fragmented assemblies, we have two flavours of the pipeline.
- The plain EPO pipeline is available on the chromosome-level genomes, listed as EPO in the table above
- The scaffold-level genomes are then projected onto the EPO alignments using LastZ-net alignments, listed as EPO-Extended.
By construction, each pair of EPO and EPO-Extended alignments represent the exact same alignment of chromosome-level genomes.
Progressive Cactus
Progressive-Cactus is a next-generation aligner that stores whole-genome alignments in a graph structure. Genomes can be added incrementally, which makes it scalable to hundreds of genomes. Further details on these methods can be found in Algorithms for genome multiple sequence alignment and Cactus graphs for genome comparisons.