Genome Archive (GenArk) hubs and Dynamic BLAT

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Gerardo Perez

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Jun 1, 2021, 6:22:09 PMJun 1
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Hello Everyone,

Do you have a favorite species or a research organism for which you'd like to visualize the genomic sequence? With the recent addition of genomic assemblies for more than 1,300 species, it's possible that your favorite is now available in the UCSC Genome Browser. Check this list of new assemblies to see if yours is a click away. Each of these Genome Browser assembly hubs comes pre-loaded with several annotation tracks, gene models, and the ability to align genomic sequence to the reference assembly using the BLAT alignment tool. You can add your own data to your view of the assembly hub by uploading a custom track or creating a track hub.

We call this group of assembly hubs, the Genome Archive (GenArk). The genomes in the GenArk are sourced from NCBI RefSeq, the Vertebrate Genomes Project (VGP), and other projects. See the complete list of assembly hubs here.

GenArk assemblies can be found by searching the common name (e.g. American Beaver) or GCA/GCF accession (e.g. GCF_001984765.1) directly on the Genome Browser Gateway page. A full list can also be seen on the GenArk portal which is organized by phylogenetic groups and projects:

The number of NCBI RefSeq assemblies has been increasing each year, and we expect the trend to continue as assemblies from VGP, and other projects are released. Our next step is to add additional clades to GenArk including archaea, viruses, and bacteria.

As mentioned above, assembly hubs in the GenArk allow for sequence alignment using the BLAT tool. We extended our traditional BLAT tool to accommodate these assembly hubs and we call it Dynamic BLAT. Dynamic BLAT pre-computes index genomes files, which allows assemblies to have a BLAT server without needing it to be resident in the computer's memory. Dynamic BLAT allows us to offer BLAT services on nearly all of our GenArk assemblies, with a few exceptions due to excessive genome size.

We would like to thank NCBI RefSeq and Vertebrate Genome Project (VGP) for making these assemblies available. We would also like to thank Hiram Clawson, Mark Diekhans, Galt Barber, Lou Nassar, and Gerardo Perez, and the rest of the Browser team for their work on building the assembly hubs, creating GenArk, and extending BLAT to include these new assembly hubs.

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