SSR data can be coding base on the present of the band on acrylamide gel electrophoresis. For every primer you test, the absent band can code by 0, the first band can be code by 1, the second band can be code by 2. If you have only two locus and calling is based on presence or absence then you can use binary. Best is to use 1 and 2, the reason is some time you may have more than two alleles and then there would be three calls as 1, 2 and 3 etc..

Yes i agree with David's answer. In addition to Devit answer, 0, 1 and 2 could also be given to heterozygous alleles, homozygous donor parent allele and homozygous recipient parent allele respectively considering product size of the donor and recipient parents alleles in the agarose and or acrylamide gel. However, this is only applicable to co-dominant marker which can differentiate homozygous and heterozygous alleles.

Dear Peter Poczai,

I think that, the best results that you can calculate by the SSRs tools not from convert the allele size table of SSRs to numeric format 0,1,2 but you can calculate any results from the SSRs tools

Dear Peter,

I'm not really sure if I got your point but if you have a table of alleles of different sizes and the repeat motif (di, three, tetra, ...nucleotide) of the locus is known it should be easy. Example dinucleotide repeat: Shortest allele is n, followed by n+2, n+4, missing, n+8, .... If you know the sequence of the locus you can use the real number of repeats as numerical mark. Last but not least you can code each allele in 000010 blocks (number of all alleles and presence of a specific allele per locus and individual).

Cheers Dietmar

Dear Dr Peter

thank you for your question. But it is not clear question, is this a mqpping studies or genetic diversity. It depend on the study. For example mapping you have different scores depend on the marker results it self. Also, diversity have different scores depends on program

best regards

khaled

For mapping studies you count each allele of one certain SSR-Marker in a 1/0-Manner and just give the alleles the names like this: SSR1allele1, SSR1allele2, SSR1allele3. After this you can calculate linkage phase (repulsion/coupling) etc. and all other parameters and relations very easy in a 1/0 matrix.