[Gramene] compara-database

[ambrose andongabo (RRes-Roth)]

Dear All,
        I am currently working on setting up Brassica Ensembl(http://www.brassica.info/Brassica_rapa/Info/Index) comparative genomics database for our Brassica Ensembl. I have been talking with some people from EBI and most of them have referred me to the people working at Grammene because you have a lot of experience with setting up compara databases for plants. Currently we have core databases for Brassica rapa (the Chinese cabbage), Arabidopsis thaliana and poplar. We intend to use these genomes to generate data for our compara database. In the future we will be adding other Brassica species when the data will become available. 

I will be please if you can give me some steps I have to follow and a clue about some pitfalls I may encounter during the analysis. As of now I intend to use the following work flow

The order of work
1) Pairwise Alignments
2) GeneTree
3) Synteny
4) MSAs & conservation
5)  Family

Many thanks in advance

NB: I am really very interested in know how you performed the EPO alignment. All the steps involve and the details will be appreciated.

Cheers

Ambrose