[Bioperl-l] Re: Comparative genomics - regions of synteny and whole genome duplication

[Elia Stupka]

Some points in reply to Lukasz:

> blocks of synteny are best defined by clusters of orthologue genes on
> chromosomes.

This is the strategy that I had outlined, which leaves us with the major
question of assigning orthologues. Once orthologues are assigned
correctly, one cand do "alignments" of chromosomes, as if they were
sequences with similarities.

> just shocking. Fugu is a bit better - actually one of the major scientific
> reasons to sequence fugu was because it has small genes and little
> non-coding sequence. Perhaps if you lose all ALU's, LINE's and
> SINE's you are bound to become as ugly as... fugu ;)

Correct, fugu has very good potential for this sort of work, because it
is extremely dense, and in studied regions it has shown wonderful
conserved order.

> There is one pitfall here: genes quite frequently duplicate and you can
> get sort-of self-hites which have nothing to do with synteny.

This is the problem that has been identified to happen a lot in Tetraodon,
which will make life more difficult when annotating that genome.

Having said that if you take away all the complexity of orthologous
assignment, the alignment can be treated with standard alignment
algorythms I think, therefore we can easily cope with duplications,
insertions and deletions.

Thanks so much for the input, let's keep the discussion going, and at the
same time, let's get the code rolling :)

Elia

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