Opiniomics

bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

Excited by bacterial DNA in sweet potatoes? Check this out!

Cool paper – turns out that the genome of the sweet potato has segments of the Agrobacterium genome in it! Genuinely cool stuff.

However, I found something even more exciting!  A tiny virus genome present in huge numbers of sequenced bacteria.  Check it out:

  1. GO here: http://blast.ncbi.nlm.nih.gov/Blast.cgi
  2. Click on Nucleotide Blast
  3. Where it says “Enter accession number, gi or FASTA”, simply enter the number: 9626372
  4. Where it says “Database” make sure you choose “others”
  5. Just under there, where it says “Organism (optional)” start typing the word Bacteria, and choose “Bacteria (taxid: 2)”
  6. Click the Blast button at the bottom

OMG!  This tiny viral genome is in E coli, it’s in Acinetobacter, Desulfitobacterium, Sphingobacterium….

I’M EMBARRASSED FOR THEM! #SHAME

5 Comments

  1. yes, quite an amazing phage with broad host spectrum … There’s even a publication on its prevalence now: http://www.standardsingenomics.com/content/10/1/18
    Would be great if NCBI or EBI would integrate it into their QC submission pipline.

  2. Wow.. Even my toy mapper Antonie filters out PhiX automatically. How could they not know?!

  3. There is a lot of bad science done by people who bought sequencers but didn’t know what they were doing

  4. That is the Antonie usecase on one sentence 😉 But there are limits to how much you can protect people. In any case I try. http://bertusbeaumontlab.tudelft.nl/software.html

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