Category Archives: bioinformatics

Exploring the genomic diversity of tubeworm endosymbionts

Tubeworms are cool. (To be read only in your best (eleventh) Doctor Who voice). Although, depending on how close they are to a hydrothermal vent, they might be more on the hot side….Regardless, if you’re on the fence about how … Continue reading

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Posted in bioinformatics, Coevolution, community ecology, evolution, genomics, metagenomics, microbiology | Tagged , , | Leave a comment

Retrieving a million sequences and avoiding primer bias, a new method that might have it all

We have come a long way since the early days when sequencing was a breakthrough method initially used to identify uncultured microbes from the environment. It is now been almost three decades, in fact, since the first microbial 16S rRNA … Continue reading

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Posted in bioinformatics, evolution, metagenomics, methods, microbiology, next generation sequencing | Tagged , , | Leave a comment

Molecular ecology, the flowchart

Towards the end of last semester my department’s evolutionary genetics journal club read Rasmus Nielsen’s terrific 2005 review of tests for recent natural selection in genetic data. Nielsen provides figures illustrating the effects of a recent selective sweep and the … Continue reading

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Posted in association genetics, bioinformatics, genomics, howto, infographic, linkage mapping, next generation sequencing, phylogenetics, phylogeography, population genetics, selection | Leave a comment

Visualize your genome assemblies

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily), is a program that creates visualisations of sequence assemblies that you can interact with. When assembling a genome with your favorite assembler, you are usually building graphs, from which … Continue reading

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Diving deep: Exploring microbial communities under the seafloor

As we all sat staring at three large monitors in the front of the room, the remotely operated vehicle (ROV) Jason hung on to a borehole observatory with one hydraulic arm as the other arm plugged our sampling equipment into … Continue reading

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Posted in bioinformatics, community ecology, fieldwork, genomics, metagenomics, microbiology, transcriptomics | Tagged , , , | Leave a comment

Star Trek Discovery made a debunked genome sequence into a plot point — but that’s not nearly the worst biology goof in the franchise

Anyone who’s been anywhere near my Twitter feed in the last month knows I’m pretty darned happy with Star Trek: Discovery, the latest iteration of the five-decade-old science fiction franchise. Discovery manages to build something new with the key elements … Continue reading

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Posted in bioinformatics, genomics, horizontal gene transfer | Tagged , | 2 Comments

We have the technology. Is sequencing getting better, smaller, faster?

Okay, I know some version of the phrase “recent developments in rapid and affordable sequencing have made blah blah blah possible…” is something you’ve probably read 10,000 times. However, third-generation sequencing platforms have turned out to be pretty darn astounding. … Continue reading

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Posted in bioinformatics, evolution, fieldwork, genomics, methods, next generation sequencing | Tagged , , , | Leave a comment