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Old 03-04-2013, 03:55 AM   #1
dpolychr
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Location: Lausanne

Join Date: Mar 2013
Posts: 3
Default Identify domains in DNA sequences

Dear all,

I have the following output from a HMM.


>hg19_dna range=chr7:113770949-115775846 5'pad=0 3'pad=0 strand=+ repeatMasking=none
?V UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

?V UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

?V UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

?V UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

?V UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

and also with Ns. For example:

?V
NNNNNNNNNNNNNNNNNNNNNNNN

These are all stored in a file. I would like to identify and take those regions with Us and those with Ns and make a BED file out of those according to the coordinates that are specified above. Also to generalize for more symbols, not only two (Us and Ns) but for now two is enough. Anyone that could help???

Thank you in advance
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