Hello, everyone. At present, I plan to study the diversity and environmental distribution of bacteria belonged to the same order. Therefore, I am eager for someone to show me how to design a pair primers (16S rRNA gene or housekeeping gene) for specific amplification of bacteria within the same order.
I am looking forward to receiving the kind replys, no matter to the detailed protocal, the similar researches or references.
Best wishes.
In this case you need to know which gene is specific for this bacteria. Then design the primer. For example a putative gene
If you know the gene you want to amplify, you load through the NCBI all the sequences and you draw the primer in the conserved region.
Yang Liu for example you want to amplify the tubulin gene. You research all the sequences deposed on NCBI about tubulin of your organism. You make the alignment of all sequence and you draw the primer on the part of sequence is in common. And at the end, you blast the sequence of your primer versus all the sequence in NCBI and yiu check the specificity of your primer.
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