Genome browsers and community genome annotation

yrGATE and xGDB are tools for viewing and adding annotations to genomes.

I went to the Plant GDB page and completed the student annotation tutorial. From this site, you can be directed to download the yrGate software. You can also download, search, and assemble sequences from different plant species, as well as view plant genome annotations. Below is part of a Genome Context View of Chromosome 1 from position 1 to 25000 for Sorghum bicolor.

I also went to the xGDB page and clicked on “Gene Models” underneath “Feature Tracks”. For the first locus ID (PdomGENEr1.2-01131), I scrolled right and clicked on the button in the “Annotate it!” box to open the yrGATE annotation tool. From here, I selected different exons, found their ORFs and selected the ORF for annotation. It is important to note that different ORFs can be selected and the selected ORF is in magenta. From this point, I was unsure of what to do, but I believe that you could now annotate the gene based on blast results.

When selecting two exons next to one another in the gene below, the integrity score is .95 and the coverage is 100%. When selecting the first and third exon, the intergrity is .37 and coverage is 100%.


b2gof14/students/taynick/21oct2014.txt · Last modified: 2014/10/28 13:35 by taynick
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