matchProbePair {Biostrings} | R Documentation |
In the context of a computer-simulated 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 chromosome-specific 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.
matchProbePair(Fprobe, Rprobe, subject, algorithm="auto", logfile=NULL, verbose=FALSE)
Fprobe |
The forward probe. |
Rprobe |
The reverse probe. |
subject |
A DNAString object containing the target sequence. |
algorithm |
One of the following: "auto" , "naive-exact" ,
"naive-fuzzy" , "boyer-moore" or "shift-or" .
See matchPattern for more information.
|
logfile |
A file used for logging. |
verbose |
TRUE or FALSE .
|
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".
A BStringViews object containing the set of "theoretical amplicons".
H. Pages
matchPattern
,
matchLRPatterns
,
findPalindromes
,
reverseComplement
,
BStringViews
library(BSgenome.Dmelanogaster.FlyBase.r51) subject <- Dmelanogaster[["3R"]] ## With 20-nucleotide forward and reverse probes: Fprobe <- "AGCTCCGAGTTCCTGCAATA" Rprobe <- "CGTTGTTCACAAATATGCGG" matchProbePair(Fprobe, Rprobe, subject) # 1 "theoretical amplicons" ## 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"