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dasmoth / dalliance

Interactive web-based genome browser.
http://www.biodalliance.org/
BSD 2-Clause "Simplified" License
226 stars 68 forks source link

Other genomes #196

Open dbitton opened 8 years ago

dbitton commented 8 years ago

Hi, Your browser looks great Could it support any Ensembl genomes for example http://fungi.ensembl.org/Schizosaccharomyces_pombe/Info/Index

Cheers,

Danny

dasmoth commented 8 years ago

In principle, yes it's straightforward to set up browsers for new genomes -- see the "embedding" and "configuring" sections of the documentation.

As a minimum, you'll want the reference genome sequence (in .2bit format) and a gene-set (generally in bigBed format, although there are other options). In the case of Ensembl species, it's also possible to retrieve the gene set using the Ensembl REST APIs.

One useful addition might be to be able to retrieve genome sequences from the Ensembl REST API (not currently supported, but the Ensembl API provides the necessary endpoints for this). At this point, it should be straightforward to bootstrap a Biodalliance instance for any Ensembl species -- is this what you have in mind?

dbitton commented 7 years ago

Many thanks, Yes I would like to have Biodalliance on our webserver for the Ensembl version of S. pombe genome