[Genome] Multiple genome alignment

[Brooke Rhead]

Hello Jyoti,

Sequence is not actually stored in the chain and net tables, so the 
Table Browser can't retrieve that information from the mouse chain 
track.  Also, when you click on the mouse chain track in the Genome 
Browser, information about only the current region selected in the 
Genome Browser window is displayed; this type of info also cannot be 
retrieved from the mouse chain track in the Table Browser.

Another solution is to use the "Conservation" track, and the table 
'multiz28way' (for hg18).  The table contains pointers to a multiple 
alignment file (described here: 
http://genome.ucsc.edu/FAQ/FAQformat#format5 -- be sure to note the way 
coordinates on the negative strand are handled), which contains 
sequences for all 28 genomes in the alignment.  The Table Browser has a 
special output format available for this table: "MAF - multiple 
alignment format".  This output format returns the aligned sequences the 
region you specified in the Table Browser.

The multiple alignment in the conservation track is based on the chain 
and net tracks.  Click on the "Conservation" track title above the track 
control to read about the methods used to create the track.

If you would like to parse out sequence for only certain organisms from 
the MAF, there is a set of tools run by Penn State that can do this, 
located here:

http://main.g2.bx.psu.edu/

Look under the "Fetch Alignments" link on the left-hand side of the page.

I hope this helps.  If you have further questions, please feel free to 
contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Shah, Jyoti K. wrote:
> Dear UCSC team,
> 
> I have a question regarding your conservation track. I want to extract
> the genomic region in mouse, rat and other species which align with the
> corresponding genomic region in human species. 
> 
> When I use the human genome browser and Mouse chain track, I can see the
> chromosome and coordinates in mouse species for certain human genomic
> region. But I am unable to get the same information when I try the table
> browser. Ideally, I would like to have a table which gives the following
> fields:
> 
> Human chr 
> Human genomic start
> Human genomic end
> Human sequence
> Mouse chr
> Mouse genomic start
> Mouse genomic end
> Mouse sequence
> 
> Is it possible to extract the above using your table browser? It would
> be great if you could help me with this.
> 
> Thanks
> Jyoti
> 
> 
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