Python Bio Python Introduction

Your First Bioinformatics Program

Count nucleotides in a DNA string like "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC":

# Using .count()
a_count = dna.count("A")
c_count = dna.count("C")
g_count = dna.count("G")
t_count = dna.count("T")

print(f"  A: {a_count}")
print(f"  C: {c_count}")
print(f"  G: {g_count}")
print(f"  T: {t_count}")
print(f"  Total: {a_count + c_count + g_count + t_count}")

Key concepts:

• len(dna) — number of characters in a string
• dna.count("A") — occurrences of substring
• f"..." — f-strings embed variables directly: f"GC = {gc:.2f}%"

Loop-based approach

counts = {"A": 0, "C": 0, "G": 0, "T": 0}

for nucleotide in dna:
    if nucleotide in counts:
        counts[nucleotide] += 1

for nuc, count in counts.items():
    percentage = count / len(dna) * 100
    print(f"  {nuc}: {count:>3}  ({percentage:.1f}%)")

GC content

GC content = fraction of G + C nucleotides. Key properties:

• Correlates with higher DNA melting temperature
• Characteristic ranges per organism
• GC-rich regions often correspond to gene-dense areas in mammalian genomes

gc_count = dna.count("G") + dna.count("C")
gc_content = gc_count / len(dna) * 100

print(f"GC content: {gc_content:.2f}%")

if gc_content < 40:
    print("AT-rich (low GC).")
elif gc_content > 60:
    print("GC-rich.")