How to Determine the GC‐Content of a DNA Sequence

The guanine-cytosine content, or GC-content, of a DNA sequence indicates the percentage of nucleotide base pairs where guanine is bonded to cytosine. DNA with a higher GC-content will be harder to break apart.

Method 1
Method 1 of 2:

By Hand

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Method 2
Method 2 of 2:

Programmatically (Python 2)

  1. This article assumes that the input is in FASTA format, with a single sequence per file.
  2. For FASTA format:
    • Discard the first line of the file.
    • Remove all remaining newlines and other trailing whitespace.
     def 
 init 
 ( 
 sequence 
 ): 
 with 
 open 
 ( 
 argv 
 [ 
 1 
 ]) 
 as 
 input 
 : 
 sequence 
 = 
 "" 
 . 
 join 
 ([ 
 line 
 . 
 strip 
 () 
 for 
 line 
 in 
 input 
 . 
 readlines 
 ()[ 
 1 
 :]]) 
 return 
 sequence
  3. Iterate through the data and increment your counter as you encounter any guanine or cytosine nucleotides.
    4. 4
      def 
 
 GCcontent 
 ( 
 sequence 
 ): 
 GCcount 
 = 
 0 
 for 
 letter 
 in 
 sequence 
 : 
 if 
 letter 
 == 
 "G" 
 or 
 letter 
 == 
 "C" 
 : 
 GCcount 
 += 
 1 
 return 
 GCcount
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    5. 6
      def 
 
 main 
 (): 
 script 
 , 
 input 
 = 
 argv 
 sequence 
 = 
 "" 
 sequence 
 = 
 init 
 ( 
 sequence 
 ) 
 print 
 " 
 %.2f 
 " 
 % 
 ( 
 float 
 ( 
 GCcontent 
 ( 
 sequence 
 )) 
 / 
 len 
 ( 
 sequence 
 ))

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      Tips

      • If you're calculating GC-content by hand, be sure to double check! It can be easy to miscount, especially if you're analyzing a long sequence on paper.
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