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Old 02-06-2012, 12:21 AM   #1
ufwsse
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Default help: about the tool to analyze sequence

I need a tool to analyze the reference sequence, especially about the repeats in it.
Is MUMmer enough?
Thank you for your help!
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Old 02-06-2012, 07:38 AM   #2
adaptivegenome
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If by "analyze" you mean "find" then I would recommend TRF by Gary Benson's lab. If by "analyze" you mean "infer alleles from nextgen data" then the answer is more complicated.
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Old 02-06-2012, 06:08 PM   #3
ufwsse
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Quote:
Originally Posted by genericforms View Post
If by "analyze" you mean "find" then I would recommend TRF by Gary Benson's lab. If by "analyze" you mean "infer alleles from nextgen data" then the answer is more complicated.
But it seems that TRF only gives me the tandem repeats.
I need the information about the sparsed repeats, too.
Thank you!
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Old 02-06-2012, 06:13 PM   #4
adaptivegenome
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Quote:
Originally Posted by ufwsse View Post
But it seems that TRF only gives me the tandem repeats.
I need the information about the sparsed repeats, too.
Thank you!
So for the most comprehensive list of repetitive regions I would go for RepeatMasker. Fortunately UCSC hosts RepeatMasker runs so depending on the reference genome you might not even have to run anything.
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Old 02-07-2012, 11:03 PM   #5
ufwsse
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Quote:
Originally Posted by genericforms View Post
So for the most comprehensive list of repetitive regions I would go for RepeatMasker. Fortunately UCSC hosts RepeatMasker runs so depending on the reference genome you might not even have to run anything.
Thank you for your help!
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