Bioinfomatics (ePCR) - (Nov/19/2001 )
Perhaps this is a bit off topic but does anyone here know of an algorithm which will allow one to search a DNA database(such as Genbank) using two oligos, and allowing you to define the length allowed between them. Sort of anin silico version of PCR. NCBI has an ePCR set up but it is for searches in the opposite direction (search a sequence against a database of primer pairs. Thanx
You could use findpatterns in GCG (if you have access to it) or try EMBOSS http://www.uk.embnet.org/Software/EMBOSS/ .
The program primersearch (in EMBOSS) is suitable if you are searching against a limited database, but is not applicable to searching all of EMBL as it would take too long. But STSsearch or fuzznuc may work. EMBOSS is available through the HGMP or there is a PISE interface online available through the Pasteur institute or from David Bauer http://ubigcg.mdh4.mdc-berlin.de:8080/ Aedin
Are you interested in ePCR ??
It seems to me there is no such algorithm or program for your purpose. The ePCR program is for mapping STS. I understand that what you needed is to blast genome databse using two oligos ( they are primers for either PCR or RT-PCR) and return matches which should at the same chromosome and within a distance specified by you. It's pretty simple to implement in terms of algorithm.
Perhaps it is time someone wrote such a program.
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you can do BLAST by taking OLIGO1nnnOLIGO2 (typing the sequence of your first oligo, some N's in between and then the second seq), then you'll see where your oligos match and at which positions they hybridize to the target seq. I hope you meant this type of problem.
This type of program finally came out, check this one
Here comes me-PCR (Multithreaded Electronic PCR) which adapted the originally described electronic PCR (e-PCR) algorithm to perform string searches more accurately and much more rapidly than previously possible.
Free download at http://genome.chop.edu/mePCR/
for AIX, OS X, Solaris, Linux, and Windows
Medline abstract describes me-PCR is here:
I don't think we need such a program (althought it is fine if we have one). What I do is to blast two oligos at the same time against nt database at genebank. If both primers hit the same gene you will be able to calculate the length of your PCR products.
Hope this help,