Description of "Multiplex" macro:
This macro is designed to give you an idea of the possibility of
"multiplexing" PCR primers. It will check for primer dimers
between all pairs of primers, and calculate what I call the "3'
complimentarity". This is just a fancy score to see if the three
prime ends stick together. Simple put, a match counts for one point, a
mismatch counts for -1 point. The macro will construct a table with the
maximum 3' complimentarity of each primer, then make a graphic of each pair that
score equal to or greater than your limit. I like to set this at 3 for a
start. The macro can also calculate the melting temperature of your
primers, and give an output of the difference between each primer.
Obviously, Tms should be similar for each primer, or the PCR may not
work. I don't want to get to far into the mechanics of PCR
here. If you are reading this, you should have a rudimentary idea of what
is good and not good in PCR mixes! Again, I like to set this at 3
degrees. The formula used for calculating melting temperature is as
follows:
Tm = ((c + g) * 41 - 650)/Len(primer)+ 69.3
I am contemplating adding the module that will blast your primers as
well. If this sounds interesting, mail me, and if enough people are
interested, I will add it in. It is ready to go, so it won't take
long. However, you will need to be able to set up the blast client on your
own computer. Unfortunately, they (NCBI) have made some changes to the
blast client, and it doesn't work the same as when I originally wrote the macro
in February of 2001! However, it does work, even if the results are a bit
difficult to sift through...
Platforms tested:
Windows 98, NT4, ME, 2000
Runs in Excel 98 and 2000.
This macro has been developed by David Cox.
Please use the tools available at The
Macroshack at bioinformatics.org
for comments, suggestions, and bugs.
Instructions
on using the macro.
Download
the macro.
Back to the program list.
This page was last updated on: August 28, 2002
by David G. Cox