[Bioperl-l] Re: Comparative genomics

[Dr. S.A.J.R. Aparicio]

Hi Elia
We really need this.

The key first step is definitely obtaining accurate automated alignments.
Without this no amount of tree inference will be sound. It would be a real
plus not only to be able to use these for the trees but to be able to see
the alignment with the tree object.

Sam 
On Fri, 28 Sep 2001, Elia Stupka wrote:

> Hello,
> 
>    during my week in Singapore we had some interesting discussions over
> genome comparisons. The take home messages seemed to be:
> 
> 1-one cannot do anything serious about orthologue/homologue/paralog
> detection with sequence similarity alone
> 
> 2-To get good scientific results (read research project) one needs one or
> more researchers actually going down there and analysing families with
> the help of phylogenetic trees, and spending considerable time and brain
> on figuring out what is what.
> 
> Over in Singapore, we are going to try and develop a two-track system. On
> one hand we will have a postdoc looking at each gene family, trees, etc.
> in detail as per point 2. On the other hand we obviously want to get
> something as good as possible to run automatically as part of the
> ensembl pipeline.
> 
> It turns out that phylogenetic trees have a nice flatfile format, and can
> be parsed. We'll write the db schema, object layer,etc. to store those
> phylogenetic trees in the db. Please shout if similar things exist
> already, I am thinkig of adding them to bioperl.
> 
> Once those trees are in the db, we hope to write a magic OrthologueFinder
> which will take into account protein families, genomic location,
> phylogenetic tree structure, sequence similarity, and assign orthologues.
> As far as I am aware the question hasn't been tackled in an automated way
> yet, so probably we will find out what is doable, and how good the
> approach is once we get the data rolling...
> 
> Once the ortholgoues are identified we could also have a
> GeneClusterFinder, which looks at a gene and its ortholgoues, and walks on
> the sides of them to look for conserved gene clusters.
> 
> Comments?
> 
> Elia
> 
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