Hi, there,
I'm a beginner in UCSC genome browser, and I'm attempting to find out
Rat homolog regions with Mouse genomic coordinates.
The query composites of thousands tuples like this, the db version is *mm8*:
chrX 138292125 138297400
What I want is like this, the db version is Rat* Rn4*:
chrX - 35494226 35500120
I've already tried two methods, but both of them are not perfect:
1. In the table browser, Mammal -> Mouse -> Comparative Genomice -> Rat/Net
-> input coordinate restrictions
Pros: Batch download is available in this method
Cons: The derived regions are actually highly homolog sub-regions within
the query Mouse region,
however, what I need is a single Rat region that can be
considered as a homolog gene to the query Mouse region.
2. In the genome browser, Comparative Genomics -> Rat Full -> Click on the
net alignment -> See the alignments
Pros: The two regions are mapped, and a side by side alignment is also
shown.
Though the Rat coordinates are not clearly displayed, it can be
infered from the alignments.
Cons: Batch download is not available, I have thousands of Mouse regions
to query...
Other methods:
I'm also thinking of do the mapping manually, or use PHP to search the
result pages of the side by side alignment.
But before doing that I have to make sure there's not an efficient way
to do this task~
Could anyone tell me what tool I should use please...?
Thank you!
--
Ao Zhou
Ph.D. Student,
Bioinformatics Program,
School of Informatics, IUPUI
Tel: 317-372-7004
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