The Genome Browser Agreement guarantees consistency between major projects. This allows users to attach and view their files in any genome browser. BAM, it is important to have consistent genomic coordinates across the genome browsers. With the increasing use of big data file formats eg. Ensembl, NCBI and UCSC make a joint decision on which assembly to annotate, in consultation with the species community where possible.įind out more about how genome assemblies are put together and how we use them in Ensembl: For some species, more than one genome assembly has been produced. We select species to annotate on a case-by-case basis according to a number of factors such as: phylogenetic position, assembly quality, model organism, availability of species-specific sequence data (eg. This means that any region may contain alleles that are rare or even private to that individual.Įnsembl does not produce genome assemblies, instead we provide annotation on genome assemblies that have been deposited into the INSDC (GenBank, ENA, DDBJ) and are publicly available. Some assemblies are made up of sequences from multiple individuals (such as human), while some from a single individual (such as cat), however each section of sequence comes from one individual. This always creates some gaps and errors. Because we are not able to sequence along the complete length of a chromosome, each chromosome assembly is made up of short stretches of sequenced DNA pasted together. If you have any other questions about Ensembl, please do not hesitate toĬontact our HelpDesk.A genome assembly is a computational representation of a genome sequence. For example, the first minor assembly release to become available for GRCh38 will be called GRCh38.p1. When we update GRCh38 to the latest patch release, the assembly name is appended with the patch number. Instead, we're adding additional alternate sequences to the assembly that can be swapped in on request. By default, the chromosome coordinates do not change when we update the human assembly to the most recent minor release. We incorporate these assembly updates, known as " patches" into GRCh38, as we did for GRCh37. The GRC will produce minor assembly releases to GRCh38 on a regular basis. This will redirect you to the new region in the latest assembly You can convert old coordinates to new ones via our Rest API or you find the new coordinates by simply adding the old assembly name into the address bar on the Ensembl browser webiste. You may have stored a genomic location on NCBI36 or GRCh37, and want to know where the equivalent region is on GRCh38. To link to a specific Ensembl archive site, remember to use the Permanent Link (found at the bottom left of each page) eg.įinding the new coordinates for your region of interest In addition to the previous GRCh37, Ensembl release 54 contains the older human assembly NCBI36, which is referred as NCBI36/hg18 by UCSC. If you are looking for older assemblies, try the Ensembl archive sites. Linking back to a previous Ensembl release: The data in this archive is based on the Ensembl 75 data. We maintain a l ong-term archive of the previous assembly of the human genome, GRCh37, with BLAST/BLAT, VEP and BioMart. UCSC refers to the recent human genome as GRCh38/hg38. This current major assembly release is called GRCh38. What human genome assembly and coordinate system is Ensembl using?Įnsembl uses a one-based coordinate system, whereas UCSC uses a zero-based coordinate system.Įnsembl uses the most recently updated human genome housed at the GRC.
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