Module 8: Complete Genome comparison
Module 8: Complete Genome comparison
Objective:
Study the sinteny among sequences of different species.
Script
Exercse 1:
Study the synteny between the sequences of Chlamydia muridarum (AE002160) and Chlamydia caviae (AE015925). Make a dotplot diagram similar to the one in Figure 8.3 in the textbook. Discuss the inversions that can be observed in the generated diagram.
Hints.
Tool to find ORFs: ORF Finder
http://www.ncbi.nlm.nih.gov/projects/gorf/
Select the "300" options (in front to the button " redraw"), to define the minimum number of nucleotides that an ORF must have, and click "redraw". After getting the result, save it to a file so that it can be read by python.
Do the global alignment between the ORFs . The penalty for gap insertion must be 5. The substitution matrix must contain 1 in the main diagonal and -1 in the other positions, as shown below
| A | C | G | T | |
| A | 1 | -1 | -1 | -1 |
| C | -1 | 1 | -1 | -1 |
| G | -1 | -1 | 1 | -1 |
| T | -1 | -1 | -1 | 1 |
Exercise 2:
Select synteny block present in the graphic from the previous exercise to produce a phylogenetic footprint. Choose a region where there is at least three ORFs . Is it possible to identify intergenic regions in the graph? If so, mention the parts where they occur.
Observations:
Generate a graph similar to the Figure 8.4 (p. 137). For this, use a sliding window of 75 bp.
To calculate the level of conservation, use the global alignment.
Good work!