Sequence analysis

Calculate the GC% of a sequence

In molecular biology and genetics, GC-content (or guanine-cytosine content, GC% in short) is the percentage of nitrogenous bases on a DNA molecule that are either guanine or cytosine (from a possibility of four different ones, also including adenine and thymine).

Using BioPython:

>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> from Bio.SeqUtils import GC
>>> my_seq = Seq('GATCGATGGGCCTATATAGGATCGAAAATCGC', IUPAC.unambiguous_dna)
>>> GC(my_seq)
46.875

Using BioRuby:

bioruby> require 'bio'
bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
==> "atgcatgcaaaa"
bioruby> seq.gc_percent 

==> 33

Using R:

# Load the SeqinR package.
library("seqinr")
mysequence <- s2c("atgcatgcaaaa")
GC(mysequence)

# [1] 0.3333333

Using Awk:

echo atgcatgcaaaa |\
awk '{dna=$0;  gsub(/[^GCSgcs]/,""); print dna,": GC=",length($0)/length(dna)}'

# atgcatgcaaaa : GC= 0.333333