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Posted
joy123, on 29 March 2012 - 10:45 AM, said:
Sorry to confuse you. Yes, I want to test the level of a specific bacteria that I know the 16srRNA sequence. I have problem with designing the bacteria specific primers so I posted this poster to get some help.
According to my understanding, I need to find the variable regions of the 16srRNA sequence, and then design primers based on these variable regions. And then, I should check the primer specificity on "ribosomal database project" -->"probe match". Am I correct?
But I don't know how to find the variable regions. Sorry I have checked the links you showed me, but still not so clear how to find the regions (I tried some softwares but they don't work). Are there free online tools to do it? Would you please give me more clue?
Thanks a lot!
According to my understanding, I need to find the variable regions of the 16srRNA sequence, and then design primers based on these variable regions. And then, I should check the primer specificity on "ribosomal database project" -->"probe match". Am I correct?
But I don't know how to find the variable regions. Sorry I have checked the links you showed me, but still not so clear how to find the regions (I tried some softwares but they don't work). Are there free online tools to do it? Would you please give me more clue?
Thanks a lot!
Have you compared this sequence with the general primers allready?
Take for example:
http://www.ncbi.nlm....73153&to=474707 (16S RNA seq of Staphylococcus aureus RF122) And now use the B27F primer, see if you can find this primer in that sequence...
you should be able to find it...
now think about it: its a general primer for the conserver region.. then where is the "non conservered" region...
Do the same excercice with your bacteria!
Find the 16S rna, see where the random primers bind and then think wether you can make a primer for not conservative region...
Have you done a search on "hypervariable regions of the 16S RNA" of your bacterium?
