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Primer design

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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Primer design

Postby NathanKAPOW » Fri Dec 16, 2011 1:02 am

Hi, first of all guys, i do not expect you guys to do my work for me, i just would like a clearer understanding of what i am suppose to learn or direction toward what i should be looking at. I have been given a computer based assignment regarding primer design. I have found my nucleotide sequence, ran them through the yeast genome software and it came up with a set of primers. Now i have to calculate the approximate length of the amplified sequence. with the following criteria to be noted : housekeeping gene has to be amplified at the same time, same sample etc, target mRNA should produce a DNA distingushable with housekepper and taq polymerase adds 100 bp per min.

I have been able to do 80% of the task, i am confused as to how i calculate the lenght of the amplified sequence, do i substract the starting point of the primers (offset) from the total size of the selected sequence?

Any help or reply would be highly appreciated

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Postby JackBean » Fri Dec 16, 2011 12:52 pm

length of amplicon = position of rev primer - position of fw primer

Cis or trans? That's what matters.
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Postby tranglee » Tue Dec 20, 2011 3:49 am

you should use some software to count it, example: BioEdit...
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