Retrogenomics WWU Muenster
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UCSC2FASTA Converter


  • Either start the application directly from the left menu
  • or download the application here and start by typing
    java -jar ucsc2fasta.jar
    If problems occur it may be related to the memory. You migfht encrease memory by adding -Xmx=1024m as a upper boundary of memory of 1 GB.
    java -Xmx=1024m -jar ucsc2fasta.jar


There will be a folder called .bioinf in your home directory and inside a file UCSC2FASTA.ini. If you need to adapt the species just add a line with the species needed like
If you do not specify any species, the following is the default
species=Human, Chimp, Bonobo, Gorilla, Orangutan, Gibbon, Rhesus,Crab-eating macaque, Pig-tailed macaque, Sooty mangabey, Baboon, Green monkey, Drill,Proboscis monkey, Angolan colobus, Golden snub-nosed monkey, Black snub-nosed monkey, Marmoset,Squirrel monkey, White-faced sapajou, Ma's night monkey, Tarsier, Bushbaby, Coquerel's sifaka,Mouse lemur, Sclater's lemur, Black lemur, Malayan flying lemur, Chinese tree shrew, Tree shrew,Squirrel, Lesser Egyptian jerboa, Prairie vole, Chinese hamster, Golden hamster, Mouse, Rat,Naked mole-rat, Guinea pig, Chinchilla, Brush-tailed rat, Rabbit, Pika, Pig, Alpaca,Bactrian camel, Dolphin, Killer whale, Tibetan antelope, Cow, Sheep, Domestic goat, Horse,White rhinoceros, FelCat8, Dog, Ferret, Panda, Pacific walrus, Weddell seal,Black flying-fox, Megabat, Davids myotis, Big brown bat, Hedgehog, Shrew, Star-nosed mole,Elephant, Cape elephant shrew, Manatee, Cape golden mole, Tenrec, Aardvark, Armadillo,Opossum, Tasmanian devil, Wallaby, Platypus, Saker falcon, Peregrine falcon,Collared flycatcher, White-throated sparrow, Medium ground finch, Zebra finch, Tibetan ground jay,Budgerigar, Parrot, Scarlet Macaw, Rock pigeon, Mallard duck, Chicken, Turkey,American alligator, Green seaturtle, ChrPic2, Soft-shell Turtle, Spiny softshell turtle, Lizard,X. tropicalis, Coelacanth, Tetraodon, Fugu, Tawny puffer fish, Nile tilapia,Princess of Burundi, Burtons mouthbreeder, Zebra Mbuna, Pundamilia nyererei, Medaka,Southern platyfish, Stickleback, Atlantic cod, Zebrafish Mexican tetra, Spotted gar, Lamprey