Article Predicting polymorphic EST-SSRs in silico
Can we use following motifs for EST-SSR marker development?
1. dinucletide, three time repeat eg. ATATAT
2. trinucloetide, Three time repeat eg. ACTACTACT
3. tetranucleotide, three time repeat eg. TGGTTGGTTGGT
Dear Rahul,
Yes we can use all types of Motifs for SSR-Development but it ultimately depends on your further requirement. I would further suggest you to read few papers related to SSR-development they will clearly indicate the purpose.
Dear Rahul,
For dinucleotide,better to have repeat motifs 6 or more , tri, teta penta 5 and above, as thee will be variable and you will find alternate alleles, for downstream apllications. You may read our papers on the topic.
Dear Rahul,
if you have time, You can read my another research article, on SSR's marker. I hope, it would be easy for you to understand the idea of selecting new alleles and absent alleles. Please search the reference bellow. Good luck
Identification and Genetic Diversity Analysis of Chinese Sugarcane (Saccharum spp. Hybrids) Varieties using SSR Markers. Tropical Plant Biology, pp.1-10. https://doi.org/10.1007/s12042-017-9195-6
Dear Rahul,
You can go through
Mol Biol Rep. 2012 May;39(5):5921-31. doi: 10.1007/s11033-011-1404-z.
Development of EST derived SSRs and SNPs as a genomic resource in Indian catfish, Clarias batrachus.
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