Author Archives: Brant Faircloth

Lego my regex

Posted on 2 Dec, 2011 by Brant Faircloth

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 | Leave a comment

A penny for your method: Nutator

Posted on 2 Dec, 2011 by Brant Faircloth

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 | Leave a comment

Dr. Prepper

Posted on 5 Nov, 2011 by Brant Faircloth

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 | 5 Comments

Easing the pain of titration

Posted on 21 Sep, 2011 by Brant Faircloth

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 | 3 Comments

A penny for your method: Plate sealers

Posted on 8 Apr, 2011 by Brant Faircloth

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 →

Posted in howto, methods | 1 Comment

Get your protein

Posted on 3 Apr, 2011 by Brant Faircloth

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 | 2 Comments

A penny for your method: PCR cleanup

Posted on 19 Feb, 2011 by Brant Faircloth

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 →

Posted in methods | Tagged | 12 Comments

Get you some homologs*

Posted on 14 Jan, 2011 by Brant Faircloth

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. Continue reading →

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Code rongorongo*

Posted on 27 Oct, 2010 by Brant Faircloth

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. Continue reading →

Posted in software | 4 Comments

Essential programmatic tools

Posted on 11 Jul, 2010 by Brant Faircloth

There are essentials, and there are essentials. Here are several bioinformatics software libraries that I use on a daily basis Continue reading →

Posted in bioinformatics, software | 4 Comments