ANI are you okay? Are you okay ANI?

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.

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.

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.

KEGGWatch, part I

In which I attempt to visualise metabolic maps for comparative genomics, and lead up to making a contribution to Biopython.

Jambiguity

In which a blog post is brought to you by the letter 'J', but should probably have been 'X'-rated.