| Project | Rearrangements in genomes with unequal content |
|---|---|
| Date | 02/06/05 |
| Version | 1.0 |
| Purpose of Meeting | To discuss the inital approach to the project |
| Supervisor present | Leong Hon Wai, Guillaume Bourque |
Dr Bourque explained some of the finer points of the MGR algorithm, such as why it was neccessary that the trees be addictive, how the algorithm deals with the situation in which it runs out of “good” rearrangement operations for > 3 genomes.
In the literature, genomes with unequal content usually refers to the situation where the homologous blocks are duplicated and when the genomes contains different sets of homologous blocks. Dr Bourque confirmed that for this project, we will not be dealing with duplicated blocks but only with the case where the genomes may contain different sets of blocks.
Dr Bourque also explained the significance of obtaining the ancestral gene orders in the reconstructed phylogenetic tree. He mentioned that the biologists are interested in looking at which segments of the genomes are conserved between the ancestral genome and the modern genome. Such conversation is an indication that these segments are important to the organism and may warrant further biological studies.
Prof Leong suggested we should perform some simple experiments and do some exploratory analysis of the effects that insertion/deletion of synteny blocks have on the recovered phylogenetic tree and on the gene order of the ancestral genome
Dr Bourque explained that it takes a significant amount of processing to convert the raw biological data into the sequence data which is used in the MGR algorithm. Some of the data he used were obtained directly from the biologists he worked with. He agreed to provide us with the processed biological data but for the moment he suggest that we try to work on simulated data.