check_filter: Check and filter invalid base of nucleotide sequences

In TmCalculator: Melting Temperature of Nucleic Acid Sequences

Check and filter invalid base of nucleotide sequences

Description

In general, whitespaces and non-base characters are removed and characters are converted to uppercase in given method.

Usage

check_filter(ntseq, method)

Arguments

ntseq	Sequence (5' to 3') of one strand of the DNA nucleic acid duplex as string or vector of characters
method	TM_Wallace: check and return "A","B","C","D","G","H","I","K","M","N","R","S","T","V","W" and "Y" TM_GC: check and return "A","B","C","D","G","H","I","K","M","N","R","S","T","V","W", "X" and "Y" TM_NN: check and return "A","C","G","I" and "T"

Value

Return a sequence which fullfils the requirements of the given method.

Author(s)

Junhui Li

References

citation("TmCalculator")

Examples

ntseq <- c("ATCGBDHKMNRVYWSqq")
check_filter(ntseq,method='Tm_Wallace')
check_filter(ntseq,method='Tm_NN')

TmCalculator documentation built on March 18, 2022, 6:10 p.m.