seqinr (version 1.0-1)

G+C Content: Calculates the fractional G+C content of nucleic acid sequences

Description

Calculates the fraction of G+C bases of the input nucleic acid sequence(s). It reads in nucleic acid sequences, sums the number of 'G' and 'C' bases and writes out the result as the fraction (in the interval 0.0 to 1.0) of the length of the whole sequence. Global G+C content GC, G+C in the first position of the codon bases GC1, G+C in the second position of the codon bases GC2, and G+C in the third position of the codon bases GC3 can be computed.

Usage

GC(seq)
GC1(seq)
GC2(seq)
GC3(seq)

Arguments

seq

any nucleic acid sequence

Value

• GC returns the fraction of G+C as a numeric vector, GC1 returns the fraction of G+C at first codon position as a numeric vector, GC2 returns the fraction of G+C at second codon position as a numeric vector, GC3 returns the fraction of G+C at third codon position as a numeric vector.

References

� citation("seqinr")

Examples

s=s2c("agtctggggggccccttttaagtagatagatagctagtcgta")
   GC(s)
   GC1(s)
   GC2(s)
   GC3(s)