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...
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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