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Old 06-04-2013, 12:06 PM   #1
NGS_New_User
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Exclamation microsatellite query

Hello wise people!

I have approx 10,000 microsatellites that I obtained from some assembled dna of a non-model organism. I selected a subset of the microsatellites including 50bp of the right and left flanking sites.
My intent is to use this subset as a query to search in sequenced dna data from a number of sample populations and see if I can find similar sequences in the different popns.

I am trying to think of a way to do this, does anyone know of a program/software (or a combination of different programs) that can achieve this? For those who use CLC gwb, any ideas?
I was thinking of mapping each popn to the microsatellite+flanking seqs (use the microsatellite seqs as reference), extracting a consensus sequence, then aligning that sequence back to the microsatellite seq. Is that a good way or what?
Please help...
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Old 06-04-2013, 12:13 PM   #2
vivek_
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Out of curiosity, can you please tell me how you identified the microsatellite regions? Any specific tool or method?
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Old 06-04-2013, 12:42 PM   #3
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Quote:
Originally Posted by vivek_ View Post
Out of curiosity, can you please tell me how you identified the microsatellite regions? Any specific tool or method?
I found a program online called phobos, that's the one I used. There is also TRF and msat commander but I haven't tried using those ones yet.
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Old 06-04-2013, 01:16 PM   #4
JackieBadger
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How large is your subset that you want to investigate?
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Old 06-04-2013, 01:38 PM   #5
vivek_
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Quote:
Originally Posted by NGS_New_User View Post
I found a program online called phobos, that's the one I used. There is also TRF and msat commander but I haven't tried using those ones yet.
Thanks for that. TRF seems to have been used in the 1000 genomes analysis as well.
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Old 06-04-2013, 02:35 PM   #6
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Quote:
Originally Posted by JackieBadger View Post
How large is your subset that you want to investigate?
I am first starting with a small group ie 10 sequences, each sequence is approx 150bp (ie the left flank region + repeat motif + right flanking region). The size of one of the popns that I want to search in is approx 1.8million sequences.
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