[Genome] question regarding In-Silico PCR

Braithwaite, Adam Braithwaite.Adam at mayo.edu
Tue Nov 14 09:51:51 PST 2006


Hi I have a question regarding the In-Silico PCR facility on the UCSC website. Occasionally if I run the PCR, no matches will be returned. However, if I Blat the entire predicted PCR product on UCSC, I can find the same sequence including the primers used.
 
For example:
F primer: GAGAAGGAAGGAACGAAGGAA
R primer: AGACCATCCTGGCTAACACG
 
These primers give no result on the In-Silico PCR facility, however Blating the amplicon gives this result:
http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr4:92073218-92073581&db=hg18&ss=../trash/hgSs/hgSs_genome_4c5f_a00e20.pslx+../trash/hgSs/hgSs_genome_4c5f_a00e20.fa&hgsid=80571670
 
...a PCR product of 364bp size, chr4:92,073,218-92,073,581.
 
Why do some primer combinations give no result with the In-Silico PCR, when there are in fact possible PCR products in the genome?
 
Regards,
 
Adam Braithwaite
Dr Farrer Lab
Mayo Clinic Jacksonville


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