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

[Rachel Harte]

Hello Intikhab,

The multiple alignment is created from pairwise alignments of the whole
genomes of each of the yeast species to the Saccharyomcyes cerevisiase
genome. Each alignment is relative to the + strand of Saccharyomcyes
cerevisiase. However, alignments could be to the - strand of regions from
the other genomes due to genome rearrangements in the evolutionary history
of these species. The most conserved regions are likely to be exons but
regulatory regions such as promotors and other regions of the genomes that
have an important function are also likely to be conserved. Therefore it
should not only be exons that show conservation.

If you have located the region of the promoter for YLR089C then the
sequence in the multiple alignment will be on the + strand for S.
cerevisiae and you would need to reverse complement the sequences to find
out what they would look like for the - strand alignment of S. cerevisiae
to the other genomes. Is it the maf file that you downloaded for the 7
species multiple alignment e.g. chr1.maf? The explanation of the MAf
format is here:
http://genome.ucsc.edu/FAQ/FAQformat#format5

Also, if you look at the track for this data (Conservation) in the S.
cerevisiae Genome Browser and then zoom in until you see the nucleotide
sequence in the track, then if you are looking a genes that are on the -
strand, you can see the sequence on this strand but clicking on the arrow
at the top left corner of the Browser image in line with the genome
coordinates. This will then show you the reverse complemented sequence
i.e. sequence for the - strand.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Thu, 17 May 2007, Intikhab Alam wrote:

> 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
>
> _______________________________________________
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>