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matching SNP finger printing results


Mar 9, 2013, 10:28 PM

Views: 574
matching SNP finger printing results

Hi dear all,
we finger printed our plants germplasm (5854 plants) with 44 SNP markers. we got SNP results in biallelic format i.e AA GG CC TT like this, now i want to purify my germplasm based on those SNP results, If particular SNP showing same allele like AA against plant I.Ds it means all those plants are pure against that particular markers like this i have to compare one plant with all 44 SNP markers and express them in percent purity. This experiment is like genetic purity test. Can any one help me how to solve this in PERL? I tried but not succeed. Here i am attaching my sample file.
Thanks in advance,
Attachments: compare.xls (18.0 KB)


Mar 10, 2013, 2:02 PM

Views: 563
Re: [genetist] matching SNP finger printing results

can you post the code you have come up with? Have you looked in to the Bioperl modules which could make things easier for you?