Ensemble chain file download

This page contains links to sequence and annotation downloads for the genome assemblies featured in the UCSC Genome Browser. For access to the most recent assembly of each genome, see the current genomes directory. To view descriptions of annotations, use the "describe table schema" button in the Table Browser. Previous versions of certain data are available from our track archive. To view restrictions specific to a particular data set, click on the corresponding download link and review the README text.

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For information on commercial licensing, see the Genome Browser and Blat licensing requirements. The source and executables for several of these products can be downloaded or purchased from our online store. Precompiled executable binaries are available for installing a local mirrored copy of the Genome Browser website on your web server, eliminating the need to compile the entire source tree.

If you encounter difficulties with slow download speeds, try using UDT Enabled Rsync UDR , which improves the throughput of large data transfers over long distances. The bit and bit versions can be downloaded here. The utilities directory offers downloads of pre-compiled standalone binaries for:. For example, you can find the underlying mayZeb1. These links also display under a column titled "UCSC version" on the conservation track description page.

Some files in the browser, such as bigBed files, are hosted in binary format. Also, the same format is used to dump whole-genome multiple alignments as well as gene-based multiple alignments and phylogentic trees used to infer Ensembl orthologues and paralogues.

MAF files are provided for all pairwise alignments containing human GRCh38 , and all multiple alignments. The MAF file format is described here. This is updated daily. Search terms. Search Ensembl Plants. Search Ensembl Genomes. Search all species. Search EBI. In this section. API Code If you do not have access to git, you can obtain our latest API code as a gzipped tarball: Download complete API for this release Note: the API version needs to be the same as the databases you are accessing, so please use git to obtain a previous version if querying older databases.

Database dumps Entire databases can be downloaded from our FTP site in a variety of formats. You can customise this list via our home page. Get help Using this website Documentation Adding custom tracks Downloading data. Follow us Blog Twitter. Personal Data. Arabidopsis thaliana. Oryza sativa Japonica Group. The reason to release this version is that CrossMap Fix the key error problem e.

In version 0. A chain file describes a pairwise alignment between two reference assemblies. UCSC and Ensemble chain files are available:. It consists of one line per feature, each containing columns. CrossMap converts BED files with less than 12 columns to a different assembly by updating the chromosome and genome coordinates only; all other columns remain unchanged. Regions from old assembly mapping to multiple locations to the new assembly will be split. For columns BED files, all columns will be updated accordingly except the 4th column name of bed line , 5th column score value and 9th column RGB value describing the display color.

The input BED file can be plain text file, compressed file with extension of. Compressed remote files are not supported. The output is a BED format file with exact the same number of columns as the original one.

All other columns are arbitrary. All other columns will be kept AS-IS. For standard BED format 12 columns.

If any of the defined exon blocks cannot be uniquely mapped to target assembly, the whole entry will be skipped. In this case, the original bed entries include entries failed to convert were also printed out.

BedGraph format file can be converted using either CrossMap bed or CrossMap wig , however, the output formats are different:. Use CrossMap bed command to convert a bedGraph file, output is a bedGraph file.

Use CrossMap wig command to convert a bedGraph file, output is a bigWig file. If we use CrossMap bed command to convert this 3. It will be split into 74 small blocks:. Opossum Monodelphis domestica. Orange clownfish Amphiprion percula. Orangutan Pongo abelii. Orbiculate cardinalfish Sphaeramia orbicularis.

Oriental scops-owl Otus sunia. Pachon cavefish Astyanax mexicanus. Painted turtle Chrysemys picta bellii. Paramormyrops kingsleyae. Periophthalmus magnuspinnatus. Pig - Bamei Sus scrofa. Pig - Berkshire Sus scrofa. Pig - Hampshire Sus scrofa. Pig - Jinhua Sus scrofa. Pig - Landrace Sus scrofa.

Pig - Largewhite Sus scrofa. Pig - Meishan Sus scrofa. Pig - Pietrain Sus scrofa. Pig - Rongchang Sus scrofa. Pig - Tibetan Sus scrofa.

Pig - Wuzhishan Sus scrofa. Pig-tailed macaque Macaca nemestrina. Pika Ochotona princeps. Pike-perch Sander lucioperca. Pinecone soldierfish Myripristis murdjan. Pink-footed goose Anser brachyrhynchus. Platyfish Xiphophorus maculatus. Platypus Ornithorhynchus anatinus. Polar bear Ursus maritimus.

Prairie vole Microtus ochrogaster. Rabbit Oryctolagus cuniculus. Rainbow trout Oncorhynchus mykiss. Rat Rattus norvegicus. Red fox Vulpes vulpes. Red-bellied piranha Pygocentrus nattereri. Reedfish Erpetoichthys calabaricus. Ring-necked pheasant Phasianus colchicus. Round goby Neogobius melanostomus. Ruff Calidris pugnax. Rufous-capped babbler Cyanoderma ruficeps. Ryukyu mouse Mus caroli. Saccharomyces cerevisiae. Sailfin molly Poecilia latipinna.

Sheep Ovis aries. Sheep texel Ovis aries. Sheepshead minnow Cyprinodon variegatus. Shortfin molly Poecilia mexicana. Shrew Sorex araneus. Shrew mouse Mus pahari. Siamese fighting fish Betta splendens. Siberian musk deer Moschus moschiferus. Silver-eye Zosterops lateralis melanops. Sloth Choloepus hoffmanni. Small tree finch Camarhynchus parvulus. Sooty mangabey Cercocebus atys. Sperm whale Physeter catodon. Spiny chromis Acanthochromis polyacanthus. Spoon-billed sandpiper Calidris pygmaea. Spotted gar Lepisosteus oculatus.

Squirrel Ictidomys tridecemlineatus. Steppe mouse Mus spicilegus. Stickleback Gasterosteus aculeatus. Superb fairywren Malurus cyaneus samueli. Swainson's thrush Catharus ustulatus. Swamp eel Monopterus albus. Swan goose Anser cygnoides. Tarsier Carlito syrichta. Tasmanian devil Sarcophilus harrisii. Tetraodon Tetraodon nigroviridis. Three-toed box turtle Terrapene carolina triunguis.

Tiger Panthera tigris altaica. Tiger tail seahorse Hippocampus comes. Tongue sole Cynoglossus semilaevis. Tree Shrew Tupaia belangeri.