findprobe: Find probes matching sites

In helixcn/seqRFLP: Simulation and visualization of restriction enzyme cutting pattern from DNA sequences.

Description

This function could be used to search probes (primer) matching sites. Users may lower the tol value to get more precise match result.

Usage

findprobe(dna, probe, tol = 3)

Arguments

dna	The input DNA sequence.
probe	The probe(primer) to match the DNA sequence.
tol	The number of sites that do not match

Details

dna should be a character string. tol is used to adjust the matching precision and should be integer. The smaller the number, the more precise the matching results. This function is called by clipprobe() for searching the sequences that could be used in PCR.

Value

Returns a vector containing the matched sites.

Note

To be added.

Author(s)

Qiong Ding [e-mail]

References

None.

See Also

See Also clipprobe

Examples

### findprobe() example
data(fil.phy)
fas <- ConvFas(fil = fil.phy, type = "phy")
findprobe(dna = fas[2], probe = "TATTTAAC", tol = 1)

helixcn/seqRFLP documentation built on May 17, 2019, 3:37 p.m.