how I make a living: what is bioinformatics? (part #1)

I’m constantly asked to explain what I do for a living. Here is an attempt to do so in laypersons’ terms. I’ll assume my readers are non-scientists and non-engineers, but that they’ve taken a high school biology class. “Bioinformatics” is the application of mathematics and computer science to biological data, particularly molecular biology data. By […]

examining mRNA complexity by annotation region using MapReduce

I became interested in how annotated mRNA regions (e.g., 5′ UTR, coding, and 3′ UTR) vary in information content, speculating that coding regions (CDS) of transcripts will be generally more complex than other regions due to their role in specifying protein recipes. Measuring sequence complexity using Shannon entropy validated this hypothesis, at least with regard […]

test driving the Seven Bridges Genomics bioinformatics platform

I recently examined the Seven Bridges Genomics (SBG) platform, building and running a short-read alignment pipeline. Overall, I am impressed by the software. Here I describe my test of the program and then report on my investigation of how it works. Test Drive The test pipeline I devised consisted of two steps, FastQC analysis of […]

RNAfold and sequence length

I’ve been looking for a way to compare RNAfold [1] dG results for two RNA sequences, where the two sequences differ in length. My initial thought was to simply divide the computed dG’s by sequence length (i.e., normalize by sequence length) and then compare the results. The analysis presented below shows why this won’t work. […]