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 […]

Excel mangles NCBI gene symbols

Using Microsoft’s Excel for bioinformatics work sucks, but sometimes a spreadsheet is the best format for communicating results to other scientists. The program’s default behavior mangles some NCBI gene symbols when you import them from a text file. Here is how to deal with it. Suppose you have the following list of gene symbols, and […]

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. […]

comparing BLAST results by bit score ratio

I recently read that two separate BLAST alignments to the same reference sequence can be compared to each other by normalizing the alignments by the maximum bit score of the reference sequence BLASTed against itself [1]. In this procedure, the user first aligns the reference sequence to itself to find the maximum possible bit score, […]

werewolf transcriptome conjecture

Lycanthropy—the sudden transformation of individuals into wolf-human chimeras during full moon periods—remains one of the least understood medical conditions persisting today. Researchers find investigation of the phenomenon doubly confounded by social stigma (who wants to tell a scientist that they are a werewolf?) and sampling difficulty (how many werewolves will actually sit still for a […]

bioinformatics as data science

“…a new kind of professional has emerged, the data scientist, who combines the skills of software programmer, statistician and storyteller/artist to extract the nuggets of gold hidden under mountains of data.” – The Economist, 27 February 2010 [emphasis mine] The above quotation neatly summarizes the role and core competencies of a bioinformatics professional, under the […]