| Project | Rearrangements in genomes with unequal content |
|---|---|
| Date | 14/11/05 |
| Version | 1.0 |
| Purpose of Meeting | Progress update |
| Supervisor present | Leong Hon Wai, Guillaume Bourque |
In view of the problems of using “good” rearrangements for genomes with unequal content, I suggested simply using the second phase of the algorithm which is to iteratively build up the phylogeny by inserting the genomes one at a time. Dr Bourque pointed out that he would prefer the algorithm to try using “good” rearrangements first. The reason being that this step is more flexibile since it determine one rearrangement at a time, furthermore in this experience this first phase of using “good” rearrangements have a side benefit of correcting possible errors in the gene sequence of the genomes.
He suggested that we may need to relax the condition for “good” rearrangements for genomes with unequal content but we need to have a way to avoid performing the same rearrangement twice. Dr Boruque also suggested that we can make use of the information in the gene content to score the rearrangements, i.e. to conside a weighted score function for each rearrangement.
Besides GRAPPA and MGR, Dr Bourque also suggested that we look at the algorithm used in GOTREE. He recalled that the GOTREE algorithm is one of the few algorithms that is able to handle genomes with unequal content.