User:Morgan G. I. Langille/Notebook/Halophiles/2010/08/04

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OpenWetWare

  • Spent the morning learning about advanced features of OpenWetWare (drawing charts, making online presentations, etc.)

Genome Sizes

  • Trying to figure out discrepencies in the size (bp) of the halophile genomes
    • The genbank files that I downloaded awhile ago from Rob Edward's site don't match the fasta file counts. Hfx.volcanii, Hal. sin., and Hal. med.
    • ANSWER:Genbank files were created from Scaffolds (Paired end sequencing) for Hal.sin and Hal. med and these would have some extra 'N's hence the increase in bp count. I should report both "resolved" and "estimated" genome size.
    • As for the Hfx. vol. the genbank matches the NCBI (previously sequenced) genbank file, so there must have been a mess up with the gbk file that I grabbed (i.e. the one Rob posted). This doesn't really matter since we might as well use the annotations from the curated genome project. We will just report the difference in contig size to reported genome size.