XML parsing made easy: is that podcast getting longer?

Sometime in 2009, I began listening to a science podcast titled This Week in Virology, or TWiV for short. I thought it was pretty good and listened regularly up until sometime in 2016, when it seemed that most episodes were approaching two hours in duration. I listen to several podcasts when commuting to/from work, which takes up about 10 hours of my week, so I found it hard to justify two hours for one podcast, no matter how good.

Were the episodes really getting longer over time? Let’s find out using R.
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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.