gc_content: Calculate G and C content of nucleotide sequences

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

Calculate G and C content of nucleotide sequences

Description

Calculate G and C content of nucleotide sequences. The function calculates the percentage of G and C bases relative to the total number of A, T, G, and C bases in the sequence.

Usage

gc_content(input_seq, ambiguous = FALSE)

Arguments

input_seq

Sequence (5' to 3') of one strand of the nucleic acid duplex. Can be provided as either: - A character string (e.g., "ATGCG") - A path to a FASTA file containing the sequence(s)

ambiguous

Logical. If TRUE, ambiguous bases are taken into account when computing the G and C content. The function handles various ambiguous bases (S, W, M, K, R, Y, V, H, D, B) by proportionally distributing their contribution to GC content based on their possible nucleotide compositions. For example: - S (G or C) contributes fully to GC content - W (A or T) contributes fully to AT content - M (A or C) contributes proportionally based on the ratio of A to C in the sequence - And so on for other ambiguous bases

Value

Content of G and C as a percentage (range from 0 to 100

Author(s)

Junhui Li

Examples

# Calculate GC content of a DNA sequence
gc_content(c("a","t","c","t","g","g","g","c","c","a","g","t","a"))  # 53.85%

# Calculate GC content including ambiguous bases
gc_content("GCATSWSYK", ambiguous = TRUE)  # 55.56%

TmCalculator documentation built on Oct. 5, 2026, 5:08 p.m.