In which I describe Average Nucleotide Identity (ANI), which we can use to pigeonhole bacteria into conceptual boxes labelled as 'species'. And I share more code.
Sunday, 10 November 2013
Sunday, 10 March 2013
Wednesday, 13 February 2013
A Nice New Paradox
In which I work through a popular statistical puzzle/paradox (with potential implications for interpretation of large data studies). With example code.
Friday, 8 February 2013
Surely this has been done already...
In which it turns out that if it was done already, it was hiding somewhere. Also, I share a script that retrieves the corresponding nucleotide coding sequences from NCBI, given only a set of protein sequences.
Friday, 1 February 2013
KEGGWatch, part III
In which I finally get around to sharing some code, and give some examples of downloading and modifying KEGG pathway maps.
KEGGWatch, part II
In which I don't quite get around to writing a KGML parser and visualisation module (all very Tristram Shandy, this!), with a view to submitting to Biopython. This post describes some of the rationale and design choices - tune into part III for code and examples of use.
Monday, 21 January 2013
KEGGWatch, part I
In which I attempt to visualise metabolic maps for comparative genomics, and lead up to making a contribution to Biopython.
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