calculate_gc.md

Calculating GC Content

GC Content

In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). GC-content may be given for a certain fragment of DNA or RNA or for an entire genome.

GC-content may be given for a certain fragment of DNA or RNA or for an entire genome. When it refers to a fragment, it may denote the GC-content of an individual gene or section of a gene (domain), a group of genes or gene clusters, a non-coding region, or a synthetic oligonucleotide such as a primer. See More on Wikipedia

Calculation

GC-content is usually expressed as a percentage value, but sometimes as a ratio (called G+C ratio or GC-ratio). GC-content percentage is calculated as

$ GC = \frac {G+C} {Len(DNA Sequence)} \times 100% $

Applications

Molecular biology

In polymerase chain reaction (PCR) experiments, the GC-content of short oligonucleotides known as primers is often used to predict their annealing temperature to the template DNA. A higher GC-content level indicates a relatively higher melting temperature.

Systematics

The species problem in prokaryotic taxonomy has led to various suggestions in classifying bacteria, and the adhoc committee on reconciliation of approaches to bacterial systematics has recommended use of GC-ratios in higher-level hierarchical classification.For example, the Actinobacteria are characterised as "high GC-content bacteria".In Streptomyces coelicolor A3(2), GC-content is 72%

Calculating GC Content

1. Download a DNA sequence from NCBI
2. Reading and cleaning the DNA sequence.
3. Create an algorithms for calculating GC content.

Download a DNA Sequence from NCBI

You can download the dataset from NCBI. Accession ID: NM_207618.2, Enter the accession id and click on FASTA, copy all the sequence without >NM_207618.2 Mus musculus vomeronasal 1 receptor, D18 (V1rd18), mRNA.then save it as .txt file.

Reading and cleaning the DNA sequence

# Read the DNA sequence 
with open("../data/dna.txt", "r") as f: 
    seq = f.read()

seq

'GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCA\nGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCT\nCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCT\nTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCT\nCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTG\nAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAA\nACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAA\nGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGAT\nTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCA\nGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGA\nCCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTT\nTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATT\nGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGG\nTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTT\nGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTC\nACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTG\nATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT\n\n'

The output is not a clean dataset because it contains a special character("\n"). It also may contain a special character("\n"). The special characters affect our analysis and may cause errors. That's why we have to clean the dataset by removing the special characters.

# Check the DNA sequence length 
len(seq)

1175

It is incorrect! because the original length of this DNA sequence is 1157. The special characters 18. Let's clean the dataset.

# Replace "\n" character with empty space.
seq = seq.replace("\n", "")

seq

'GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCAGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCTCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCTTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCTCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTGAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAAACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAAGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGATTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCAGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGACCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTTTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATTGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGGTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTTGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTCACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTGATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT'

# Now check the length
len(seq)

1157

YES! it is the original length of the DNA sequence. But we have to remove "\r"

seq = seq.replace("\r", "")

seq

'GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCAGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCTCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCTTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCTCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTGAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAAACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAAGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGATTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCAGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGACCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTTTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATTGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGGTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTTGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTCACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTGATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT'

len(seq)

1157

Create a Function To Read Sequence File

def read_seq(inputfile):
    """
    Reads the DNA sequence file and returns as strings. Removes all the special characters.
    """
    with open(inputfile, "r") as f:
        seq = f.read()
        seq = seq.replace("\n", "")
        seq = seq.replace("r", "")
    return seq 

# Read the seq file with rea_seq function
dna = read_seq("../data/dna.txt")

dna

'GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCAGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCTCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCTTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCTCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTGAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAAACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAAGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGATTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCAGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGACCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTTTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATTGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGGTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTTGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTCACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTGATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT'

# Check length 
len(dna)

1157

Calculate GC Content

def calculate_gc_content(seq): 
    """
    Take DNA sequence as input and calculate the GC content.
    """
    no_of_g = seq.count("G")
    no_of_c = seq.count("C")
    total = no_of_g + no_of_c 
    gc = total/len(seq) * 100
    
    return gc 

calculate_gc_content(dna)

39.58513396715644

Final Code

def read_seq(inputfile):
    """
    Reads the DNA sequence file and returns as strings. Removes all the special characters.
    """
    with open(inputfile, "r") as f:
        seq = f.read()
        seq = seq.replace("\n", "")
        seq = seq.replace("r", "")
    return seq 

def calculate_gc_content(seq): 
    """
    Take DNA sequence as input and calculate the GC content.
    """
    no_of_g = seq.count("G")
    no_of_c = seq.count("C")
    total = no_of_g + no_of_c 
    gc = total/len(seq) * 100
    
    return gc 

# Read the DNA sequence file 
dna = read_seq("../data/dna.txt")
# Calculate GC Content 
result = calculate_gc_content(dna)
print(result)

39.58513396715644

So the GC content is 39.5852%