| Project | Rearrangements in genomes with unequal content |
|---|---|
| Date | 16/12/05 |
| Version | 1.0 |
| Purpose of Meeting | Discuss plans for the rest of the project |
| Supervisor present | Guillaume Bourque |
Dr Bourque suggest that we can look at the homology database at NCBI and the COG database to get a list of homologous genes. This information together with information about the positions of these genes in different genomes will allow us to extract real data sets from the information available online.
He also mentioned that perhaps an automated tool for generating genomes as a sequence of numbered genes from online sources would be a very useful tool for researchers studying genome rearrangements.
In the discussion about the “best” rearrangements algorithm, Dr Bourque pointed out that besides using the percentage of common genes to weigh the score of a rearrangement, we could also look at the minimum number of rearrangements between the genomes.
The idea is that realistic rearrangements are those which reduces the number of rearrangements between genomes which have similar content as well as between genomes which are near one another in terms of the rearrangement distance. I've taken up Dr Bourque's suggestion and will be looking into how we can incorporate information about the rearrangement distance into the score function.
Dr Bourque recalled that in order to run the original MGR program on large datasets he used the options -H5 (stop once we find a good rearrangement) and -c (condense genomes). H3 is also a heuristic option that is commonly used.