Searching for the Steamer retroelement in the ocean metagenome

/ nsaunders

Location of BLAST (tblastn) hits Mya arenaria GagPol (AIE48224.1) vs GOS contigs

Location of BLAST (tblastn) hits Mya arenaria GagPol (AIE48224.1) vs GOS contigs

Last week, I was listening to episode 337 of the podcast This Week in Virology. It concerned a retrovirus-like sequence element named Steamer, which is associated with a transmissible leukaemia in soft shell clams.

At one point the host and guests discussed the idea of searching for Steamer-like sequences in the data from ocean metagenomics projects, such as the Global Ocean Sampling expedition. Sounds like fun. So I made an initial attempt, using R/ggplot2 to visualise the results.

To make a long story short: the initial BLAST results are not super-convincing, the visualisation could use some work (click image, right, for larger version) and the code/data are all public at Github, summarised in this report. It made for a fun, relatively-quick side project.

2 thoughts on “Searching for the Steamer retroelement in the ocean metagenome”

  1. blastn would probably been a better option than the default megablast for blast +, it has to be extremely well conserved to be matched by megablast.

    • Correct. Just tried that, nothing very significant using blastn. Top hit:

      gi|662488887|gb|KF319019.1| CAMCTG_132890063 75.00 80 17 1 515 594 439 363 0.003 53.6

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