Finding Flies

I finally got around to reading last month’s Nature paper on the genomic sequence of 12 Drosophila species. In addition to being genomics research (which is my field now :), it is also looking at 12 of the couple dozen species I studied for my Ph.D. (though I was only looking at the evolution of R1 & R2 retroposons in arthropods).Interesting paper, and I might go into it more in depth later (what genomics means and doesn’t mean for evolutionary studies).

But I did get to thinking, where would I go to browse and search the genomic sequence data for these 12 species ( hey, I might want to recreate my work, though the Eickbush lab already has.. and extended). Of course there are the two browsers mentioned in the paper ;-), Flybase and UCSC Genome Browser, though UCSC doesn’t include D. willistoni as I write this. I checked the other two major general genome browsers, as opposed to species or taxa specific: Ensembl and NCBI’s MapViewer.Both Ensembl and MapViewer currently have only D. melanogaster available for browsing. This might change, these three genome browsers are adding genomes regularly. But, if you wanted to browse, compare and search Drosophila species genome data, UCSC or Flybase is where’d you go right now.

This highlights a point. We are often asked how to decide which of the three browsers to use. The first part of that answer is what species or group of species you want to look at and compare.If it’s mammalian species, Ensembl might be the right choice: it currently has 24 mammalian species, while NCBI MapViewer has 13 and UCSC Genome Browser has 11.If it’s plants, than NCBI MapViewer is your choice. Though of course there is Gramene, TAIR and other plant-specific ones, NCBI has 35 plant species, Ensembl has none and UCSC Genome Browser has only S. cerevisiae.Of course if you wanted to look at retrotransposable elements in ribosomal genes of 12 Drosophila species, UCSC Genome Browser is your best bet :D.

(oh, and if you want the ever growing list of genomes that are completed or ongoing, … 77 eukaryotes to date with over 800 ongoing, and where to get information about them, then get right over to GOLD)