If one intend to design SSR primers for a plant species with an unknown primers sequence, what is the best method for that?
For designing primer pairs to detect polymorphism ar SSR loci, it is necessary to define the DNA target sequence to be amplified during PCR. Once you have the nucleotide sequence avaiable (it can be either a sequence from your own sequence project or a sequence searched from the NCBI nucleotide data base), the “BatchPrimer3” web program (see link below) can be used to easily search and design primers to get SSR PCR amplicons and to prepare other types of PCR primers and sequencing primers in a high-throughput manner. The input of the sequence to be scanned in order to identify the primer sites and primer sequence, is flexible. The target DNA sequence can be copied and then pasted as text to the sequence box, or a FASTA file can be uploaded to the server. See attached example on the use of “BatchPrimer3” to design a primer pair for a DNA target possssing the (TG)6 SSR motif.
http://probes.pw.usda.gov/batchprimer3/overview.html
How do I design primers that will distinguish between highly homologous transcripts?
https://www.researchgate.net/post/How_do_I_design_primers_that_will_distinguish_between_highly_homologous_transcripts
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