check_filter_seq: Filter invalid bases in nucleotide sequences

In TmCalculator: Genome-Wide Nucleic Acid Melting Temperature Profiling and Multi-Omics Integration

Filter invalid bases in nucleotide sequences

Description

This function processes nucleotide sequences by converting characters to uppercase and replacing invalid bases with "". based on the specified method. The function preserves the sequence length and attributes (name and Tm) of each sequence.

Usage

check_filter_seq(seq_list, method)

Arguments

seq_list	Input sequence in 5' to 3' direction. Must be provided as: - A list of sequences with attributes (name and Tm)
method	Method to determine valid bases: TM_Wallace: Valid bases are "A","B","C","D","G","H","I","K","M","N","R","S","T","V","W" and "Y" TM_GC: Valid bases are "A","B","C","D","G","H","I","K","M","N","R","S","T","V","W", "X" and "Y" TM_NN: Valid bases are "A","C","G","I" and "T"

Value

Returns a list of sequences with the same structure as input, where invalid bases are replaced with ""

Author(s)

Junhui Li

References

citation("TmCalculator")

TmCalculator documentation built on Aug. 28, 2026, 5:09 p.m.