Different versions of the human genome in the three major genetic databases

In data analysis, it is often necessary to download the reference genome sequence of the species, when there are many databases to choose from, such as NCBI, ENSEMBL, UCSC, the three universal databases, or the species-specific database,

For example, the model bio-Arabidopsis has a dedicated database.

In NCBI, ENSEMBL and UCSC for the same species, numbering is not uniform, here is the relationship between them, taking the human genome as an example:

In NCBI, for different assembly versions, the NCBI build number is differentiated, and the same version has a slight difference between the different iteration versions,

The previous version of the human genome can be seen in the following connection,

For example, build.36.1, NCBI build number is 1, Version is 37.1, starting with build, and new naming method, GRCh37

There is a CRC organization (HTTP://WWW.NCBI.NLM.NIH.GOV/PROJECTS/GENOME/ASSEMBLY/GRC/), which is an academic group that is joined by organizations such as EBI,NCBI, A brief and unified naming of the different assembled versions of the genome, h for humans, 37

Indicates the version number, for the same version, there will be small changes, at this time with P plus number identification, such as build 37.3 is named GRCH37.P5, p for patch, patch;

At present the more commonly used version has GRCh37 and CRCh38 two versions;

In Ensembl, there are different release, such as

The human genome corresponds GRCh38 from release-76 to release-83, release-75 from release-55 to GRCh37

This can be seen from the naming method, taking release-83 as an example:

The first chromosome of the human genome is named Homo_sapiens. Grch38.dna.chromosome.1.fa.gz, where the CRCh38 is the assembled version

In the UCSC,

Hg38 Correspondence GRCh38

Hg19 Correspondence GRCh37

It is also important to note that ENSEMBL downloaded the fasta sequence, whose identifier does not contain CHR,

For example, the human genome chromosome 1th, the identifier downloaded in UCSC and NCBI is >CHR1, and ENSEMBL is >1

Different versions of the human genome in the three major genetic databases