In the context of a computersimulated PCR experiment, one wants to find
the amplicons mapped to a given primer pair.
The matchProbePair
function can be used for this: given a forward and a
reverse probe (i.e. the chromosomespecific sequences of the forward and
reverse primers used for the experiment) and a target sequence (generally a
chromosome sequence), the matchProbePair
function will return all
the "theoretical amplicons" mapped to this probe pair.
1  matchProbePair(Fprobe, Rprobe, subject, algorithm="auto", logfile=NULL, verbose=FALSE)

Fprobe 
The forward probe. 
Rprobe 
The reverse probe. 
subject 
A DNAString object (or an XStringViews object with a DNAString subject) containing the target sequence. 
algorithm 
One of the following: 
logfile 
A file used for logging. 
verbose 

The matchProbePair
function does the following: (1) find all
the "plus hits" i.e. the Fprobe and Rprobe matches on the "plus" strand,
(2) find all the "minus hits" i.e. the Fprobe and Rprobe matches on the
"minus" strand and (3) from the set of all (plus\_hit, minus\_hit) pairs,
extract and return the subset of "reduced matches" i.e. the (plus\_hit, minus\_hit)
pairs such that (a) plus\_hit <= minus\_hit and (b) there are no hits (plus
or minus) between plus\_hit and minus\_hit.
This set of "reduced matches" is the set of "theoretical amplicons".
An XStringViews object containing the set of "theoretical amplicons".
H. Pagès
matchPattern
,
matchLRPatterns
,
findPalindromes
,
reverseComplement
,
XStringViewsclass
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  library(BSgenome.Dmelanogaster.UCSC.dm3)
subject < Dmelanogaster$chr3R
## With 20nucleotide forward and reverse probes:
Fprobe < "AGCTCCGAGTTCCTGCAATA"
Rprobe < "CGTTGTTCACAAATATGCGG"
matchProbePair(Fprobe, Rprobe, subject) # 1 "theoretical amplicon"
## With shorter forward and reverse probes, the risk of having multiple
## "theoretical amplicons" increases:
Fprobe < "AGCTCCGAGTTCC"
Rprobe < "CGTTGTTCACAA"
matchProbePair(Fprobe, Rprobe, subject) # 2 "theoretical amplicons"
Fprobe < "AGCTCCGAGTT"
Rprobe < "CGTTGTTCACA"
matchProbePair(Fprobe, Rprobe, subject) # 9 "theoretical amplicons"

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
All documentation is copyright its authors; we didn't write any of that.