HI everyone:
for I have a list of regions in the human genome and want to study if
those regions have conservational counterparts in the mouse genome or
not, I download "mouse net" file from Table Browser and in this file I
found there may be two or even more "top" alignment region spanning
the same regions in the mouse genome.as a result sometimes a same
region in the human genome will have a perfect conservational region
according to one "top" alignment region and may have many gaps
according to another.
my question is which I should trust? and if there exist a better way
to study my problem please tell me (for I want to see detailed
information about alignment say regionA in the human genome may have a
conservational region in the mouse genome but many gaps on it, I want
to see the exact coordinate of the gap and match regions).
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