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:
- GO here: http://blast.ncbi.nlm.nih.gov/Blast.cgi
- Click on Nucleotide Blast
- Where it says “Enter accession number, gi or FASTA”, simply enter the number: 9626372
- Where it says “Database” make sure you choose “others”
- Just under there, where it says “Organism (optional)” start typing the word Bacteria, and choose “Bacteria (taxid: 2)”
- 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
22nd April 2015 at 9:35 am
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.
22nd April 2015 at 10:46 am
Reblogged this on themonkseal.
26th April 2015 at 10:56 am
Wow.. Even my toy mapper Antonie filters out PhiX automatically. How could they not know?!
26th April 2015 at 10:57 am
There is a lot of bad science done by people who bought sequencers but didn’t know what they were doing
26th April 2015 at 11:01 am
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