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Author Archives: Brant Faircloth
A penny for your method: AMPure Substitute
This week may stand as the most exciting week of the year for decreasing the cost of PCR cleanup, DNA cleanup, and library prep. Why, you ask? Because a great paper was published over in Genome Research by Nadin Rohland … Continue reading
Posted in howto, methods, next generation sequencing
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Lego my regex
Regular expressions are something that pretty much everyone working with more than a handful of data should take the time to learn (a handful being around 500 lines). They can easily improve your life, particularly if you’ve ever had to … Continue reading
Posted in bioinformatics
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A penny for your method: Nutator
This one requires a little ingenuity on your part (and perhaps some craft, duct tape, construction, and/or welding skills). A nutator (AKA nutating mixer or rotating mixer) is a gently rocking/rotating platform useful for continuously and gently mixing samples. They … Continue reading
Posted in howto, methods, next generation sequencing
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Dr. Prepper
Library preparation for next-gen sequencing has become a fact of life in many labs working with model and non-model organisms. The problems with library preparation are that (1) library prep is slow and (2) library prep is expensive. Generally speaking, … Continue reading
Posted in methods, next generation sequencing
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Easing the pain of titration
Quickly following up on Nick’s post re: Illumina Library Prep, Travis Glenn pointed me towards a manuscript in Nature Protocols that proposes an alternative to the oft-grumbled-about process of titrating libraries for 454/Ion Torrent sequencing: Zongli Zheng et al. Titration-free … Continue reading
Posted in bioinformatics, howto, methods, next generation sequencing
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A penny for your method: Plate sealers
You may call them plate sealers, we call them “sticky-tops” (as opposed to the rubber plate sealers we use for PCR). Whatever you call them, they seal up 96- and 384-well plates so you can store them in the fridge … Continue reading
Get your protein
This weekend, I was doing a little work on one of our projects where we are using various cpDNA genes. I really needed to get a number of protein sequences from Genbank for the products of chloroplast genes. If I … Continue reading
Posted in bioinformatics, howto, methods
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A penny for your method: PCR cleanup
Very rarely, in scientific research, do we get the opportunity to do less with more. As a result, one thing that we are good at is stretching a dollar. To (hopefully) contribute something back to the struggle, I’ve decided to … Continue reading
Get you some homologs*
Let’s assume the following scenario: you have a gene in which you are interested. You would like to find the putative location of this gene in another organism using sequence similarity searches. The question is, how do you do that? The answers are many. Here is one.
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Code rongorongo*
Open-sourcing computer programs used as part of a scientific research program is important to supporting the validity of the research conducted and enabling progress in many fields. Yet, the issue of making computer code widely available is not without complication.
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Posted in software
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