Description of optional project to accompany MCB3421

The project to accompany the course can be used for an honors conversion; or it could take the place of one of the take-home exam. If successful, it will count for 10% of the final grade.
The project will consist of finding and characterizing an intein* that has not been previously characterized, and that has invaded a bacterial virus (aka bacteriophage – meaning eating bacteria - or phage).
The project will consist of multiple steps, most of which will accompany things we do in the computer lab, plus a few additional steps.

1. Find a gene that has been invaded by an intein in some phages but not in some other closely related phages. We will use a website (called phamerator) that aligns phage genomes. We will pick 6 genomes from a cluster or subcluster of phages, and will screen them for an alignment pattern that suggests the presence of an intein
2. We will then take the protein encoded by the putatively invaded gene, and do a blast search of a phage databank (phagesdb) to confirm the presence of the intein in some of the homologous proteins
3. If this works out, we will do blast searches of a local databank of phage genomes to retrieve the DNA sequences encoding these genes (with and without the intein).
4. Run scripts to rename the sequences to include the cluster designation and the geographical location where the phage was isolated.
5. Calculate a multiple sequence alignment and separate the alignment columns into extein (the protein the hosts the intein), and the intein.
6. Reconstruct trees depicting the evolution of the intein and extein and try to infer how often the gene was transferred. We also will study the geographic location of the phages that share closely related inteins.
7. Possibly we will also study the strength of selection acting on the sequences, and the diversity of the sequences.

Steps 2, 3, 5, 6, 7 will parallel computer lab exercises, and thus provide an opportunity to apply the learned methods to a research project.

*An intein is a segment of a protein that is able to excise itself and join the remaining portions (the exteins) with a peptide bond during protein splicing. Inteins have also been called protein introns, by analogy with (RNA) introns. From Wikipedia.
In addition to the self-splicing activity, most inteins also include a homing endonuclease domain that allows them to invade empty target sites, it they are present in the same cell.
We will talk about inteins in the next couple of classes.