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”
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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