Searching for the Steamer retroelement in the ocean metagenome

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. Kurt

    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.

    1. nsaunders Post author

      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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