Rosetta easteregg

The guide to use Rosetta may be a bit, ehm, flaky, but I think it is made up for by this rather amusing comment header I found in one of its Perl script, kudos to the author.

###############################################################################
#
# MAKE_FRAGMENTS.PL 1.00 -- THE (PEN)ULTIMATE IN HOME FRAGMENT-PICKING SOFTWARE!
#
# CAUTION:  NO USER SERVICEABLE PARTS BELOW!
#
#           TO REDUCE RISK OF ELECTRIC SHOCK, DO NOT REMOVE THE COVER!
#           DO NOT ATTEMPT REPAIRS!  REFER SERVICING TO YOUR AUTHORIZED DEALER!
#           AVOID PROLONGED EXPOSURE TO HEAT OR SUNLIGHT!
#           TO REDUCE THE RISK OF FIRE OR ELECTRIC SHOCK, DO NOT EXPOSE THE
#            PRODUCT TO RAIN AND/OR MOISTURE!
#           DO NOT MOVE THE PRODUCT WHILE IN USE!
#           DO NOT LOOK AT THE PRODUCT WHILE IN USE!
#           DO NOT COMPLAIN ABOUT THE PRODUCT WHILE IN USE!
#           DO NOT DISCUSS THE PRODUCT WHILE IN USE!
#           DO NOT THINK ABOUT THE PRODUCT WHILE IN USE!
#           CLEAN ONLY WITH MILD DETERGENTS AND A SOFT CLOTH!
#           USE ONLY IN WELL-VENTILATED AREAS!
#
#           FOR EXTERNAL USE ONLY!  DO NOT TAKE INTERNALLY!
#           MAY PRODUCE STRONG MAGNETIC FIELDS!
#
#           DO NOT REMOVE THIS TAG UNDER PENALTY OF LAW.
#
#           THIS ARTICLE CONTAINS NEW MATERIAL ONLY.
#
#           THIS LABEL IS AFFIXED IN COMPLAINCE WITH THE UPHOLSTERED AND
#            STUFFED ARTICLES ACT.
#
#
# (IN OTHER WORDS:  DON'T EVEN *THINK* ABOUT CHANGING THINGS BELOW THIS POINT!)
#
###############################################################################

In vivo shuffling via heteroduplex amplicons

Bluescreen transilluminator photo showing
different shades of green.

In a previous post I discuss the heteroduplicity of epPCR plasmids. Namely often colonies in a library will have bases that have two equal variants. The most likely cause being that the amplicons do not anneal perfect and that the transformed plasmids are actually heteroduplexes. These can either divide before being corrected or are corrected by mismatch repair.
I did a sneaky experiment to see if this could be used to make protocol to shuffle mutations between variants and got a positive result, but possibly not as effective as hoped.

A note on Mutazyme and Manganese

Can Mutazyme be powered up?
Adding manganese works poorly, but stronger variants seem to be known.
(see also discussion about Mutazyme in Part I and II)

A simple hack for a phylogenetic Noah's ark dilemma

Ever had an endless list of bacterial names that needed a trim?
Ever see a tree where the bacterium chosen is not the famous one, but it's cousin? Or actually a tree where you don't recognise a single name?
The issue of picking bacteria from a list is what I call Noah's ark dilemma. This term is used generally for the biblical problem of the size of the boat required for all the animals in existence (except dinosaurs). Here I mean it picking the most meaningful bacteria from a list. In the past year, I have come to rely on a simple solution: Pubmed popularity.

Peak height variation

Sequencing a plasmid pool containing a sequence with a randomised codon can reveal the frequencies of the bases are (Acevedo-Rocha et al., 2015 ).
The problem is that sequence traces are not consistent. Some peaks are bigger than others and beyond a certain point the traces get messy. So how does that affect the prediction of the base frequencies?

Top 5 useful facts about the MDS42 strain

MDS42, also known as the Blattner strain, is a strain made in 2006 by deleting 13% of the genome of E. coli K-12 MG1655. Unfortunately, as tools go, it rivals IKEA in cryptic instruction manuals.

On error rates of Mutazyme

On a previous jocular post about the 'not for diagnostic purposes' tag on Mutazyme I mention the mutational rate of Mutazyme II. The exact mutations per kb per doubling is never mentioned in the manual, but can be extrapolated. (see also part III: Mutazyme and Manganese)