[Genome] ?'s about sequence alignments via UCSC genome

[Brooke Rhead]

Hello Aaron,

On the most recent mouse assembly (mm9, July 2007), there is a track in 
the Genome Browser called "Conservation" that shows multiple alignments 
of mouse and 29 other vertebrate species, along with measures of 
conservation.  Click on the blue track name for more details about how 
the track was made, and to display more species.

You may also be interested in the "Most Conserved" track, which shows 
predictions of conserved elements produced by the phastCons program, as 
well as the pairwise alignments of mouse against other species in the 
chain and net tracks.  All of these tracks are in the "Comparative 
Genomics" section of the Genome Browser.

If you need to find the location of your sequence on the mm9 assembly, 
you can use the BLAT tool.  Click on "Blat" in the blue bar at the top 
of the page, select the Mouse, July 2007 assembly, paste the sequence 
into the box, and hit "submit".  From there you should be able to select 
the best match to the sequence you entered.

I hope this information helps get you started.  If you have further 
questions, please feel free to write back to the genome mailing list 
address.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Aaron Fletcher wrote:
> Hi, my name is Dr. Aaron Fletcher and I am a post-doc who is trying
> to determine sequence homology throughout different species
> "evolution".   I started with a 1300 bp fragment and performed a
> BLAST search on it to narrow it down to a more manageable 161 bp
> sequence I am particularly interested in.  I was told that UCSC
> genome was a good sight to do sequence homology on.  I am not
> familiar/endowed in doing sequence homologies and would appriciate
> any help/guidance you could provide.  I only have a DNA sequence...I
> do not know if it is a coding region or not and therefore do not
> currently have a peptide sequence to compare as well.   What is the
> best way to compare my mouse sequence to other eukaryotes to
> determine conservation, etc.
> 
> Thank you in advance for your help, Aaron Fletcher
> 
> _______________________________________________ 
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