Searching for the Steamer retroelement in the ocean metagenome
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Location of BLAST (tblastn) hits Mya arenaria GagPol (AIE48224.1) vs GOS contigs
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.
Filed under: bioinformatics, R, statistics Tagged: cancer, clam, GOS, metagenomics, ocean, retroelement, steamer, twiv, virus
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