Author Archives: Brant Faircloth

About Brant Faircloth

I'm an Assistant Researcher at the University of California - Los Angeles. My interests include mating behavior, social behavior, the (immuno-)genetic basis of mate choice, genomics of non-model organisms, metagenomics, computer programming, and the integration of molecular and field biology.

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 | Leave a comment

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 | Leave a comment

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 | 5 Comments

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 | 3 Comments

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

Posted in howto, methods | 1 Comment

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 | 2 Comments

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

Posted in methods | Tagged | 12 Comments

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.

Continue reading
Posted in bioinformatics, howto | Leave a comment

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.

Continue reading
Posted in software | 3 Comments

Essential programmatic tools

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 | 3 Comments