PLNT3140 INTRODUCTORY CYTOGENETICS    

This assignment is worth 5% of the course grade.

Due Tue. Dec 3, 2024.

Note: This assignment assumes that you have already gone through the Bioinformatics Lab components on Dot matrix similarity searches. Theory: Matrix Similarity Searches  VIDEO (35:45) Tutorial: DXHOM  VIDEO (19:48)

The structure and evolutionary history of entire chromosomes can be studied using dot-matrix plots such as DXHOM. For example, comparison of an entire chromosome with itself might give a plot like that shown below:

For each of the following, show how you would use a dot-matrix plot to detect:

1) (1 point) A chromosome with an internal tandem duplication.

2) (1 point) A chromosome with an internal deletion, compared to the wild-type chromosome.

3) (1 point) A chromosome a terminal inversion, compared to the wild-type chromosome.

4) (1 point) A reciprocal translocation between two non-homologous chromosomes (you will need to draw two plots to show this).

5) (1 point) The original example oversimplified things a bit. Typically, when a self-self comparison is done using real chromosomal sequences, the figure looks more like the one below. Explain why we see these 'diamond' arrays of parallel diagonals.

Notes:

a. By convention, the X-axis is numbered 5' to 3', left to right, and the Y-axis is numbered 5' to 3', top to bottom.
b. Use numbering on the X and Y axes to indicate the orientation of each strand.