[Genome] help in seven species of Saccharomyces, Alignment and Conservation

[Intikhab Alam]

Hi,

I have been looking into the Alignment and Conservation of 
Saccharomyces genomes at your browser. Principally, I was interested 
in how the conservation look like in the intergenic regions of these 
genomes. I can explore the conservation in the browser but when I 
downloaded the alignments of these 7 organisms, it seems only the 
exons are aligned, is it the case?

Another problem I encounter is that from the browser, if I click on an 
intergenic region covered by the conservation block, it shows the 
aligned sequences from these Saccharomyces 7 organisms but do not show 
the correct strand. E.g for the promoter region of YLR089C cerevisae 
gene, it show only the positive strand though the correct sequence is 
in the negative strand.


Is it possible to get the Phastcons scores and the alignment of these 
7 organisms showing either the complete genome or only the intergenic 
regions?

Many Thanks for your help.

Intikhab

--

Dr. Intikhab Alam
Research Associate
School of Computer Science
University of Manchester
LF1, Kilburn Building,
Oxford Road Manchester, M13 9PL
United Kingdom
http://www.cs.man.ac.uk/~ialam