DNA Sequence Analysis – Python Challenge

Task 1: Counting Nucleotides

Write a function called count_nucleotides that takes a DNA sequence as input and returns a dictionary with the counts of each nucleotide (A, T, C, G).

Example:

dna_sequence = "ATGCGATCCATGACAAT"
nucleotides = count_nucleotides(dna_sequence)
print(nucleotides)
# Output: {'A': 6, 'T': 4, 'C': 4, 'G': 3}

Task 2: Finding the Complementary Strand

Write a function called complementary_strand() that takes a DNA sequence as input and returns its complementary strand. In DNA, the complementary base pairs are A-T and C-G.

Example:

dna_sequence = "ATGCGATTCA"
complementatry_dna_sequence = complementary_strand(dna_sequence)
print(complementatry_dna_sequence)
# Output: "TACGCTAAGT"

Task 3: Identifying Patterns

Within the DNA sequence we can identify patterns for the different amino acids that makes up the DNA. Each amino acid can be identified using a sequence of 3 nucleotides (called a codon).

From the diagram below we can see that the codons GTA, GTC, GTT and GTG are all valid codons for the Valine amino acid whereas AGC and AGT are the codons for Serine.

Write a function called find_pattern() that takes a DNA sequence and a pattern (e.g. a three-letter codon) as input, and returns the starting indices of all occurrences of the pattern in the DNA sequence.

Example:

dna_sequence = "ATAGCGATATCGAGCTAC"
pattern = "AGC"
positions = find_pattern(dna_sequence, pattern)
print(positions)
# Output: [2, 12]

Task 4: Transcribing DNA to RNA

DNA (Deoxyribonucleic Acid) is a double-stranded molecule with a deoxyribose sugar and the nitrogenous bases Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). It stores genetic information long-term and is primarily found in the nucleus of cells. RNA (Ribonucleic Acid), on the other hand, is typically single-stranded, contains a ribose sugar, and uses Uracil (U) instead of Thymine. RNA is involved in the transmission and expression of genetic information, playing roles in protein synthesis and gene regulation. DNA is more stable, making it suitable for long-term storage, while RNA is less stable and more reactive, fitting its dynamic roles in cellular processes.

Write a function called transcribe_DNA_to_RNA() that takes a DNA sequence as input and returns the corresponding RNA sequence. In RNA, thymine (T) is replaced by uracil (U).

Example:

dna_sequence = "ATGCTAGCT"
rna_sequence = transcribe_DNA_to_RNA(dna_sequence))
print(rna_sequence)
# Output: "AUGCUAGCU"

Task 5: Calculating GC Content

Write a function called gc_content() that takes a DNA sequence as input and returns the GC content as a percentage. The GC content is the percentage of nucleotides in the DNA sequence that are either G or C.

Example:

dna_sequence = "ATGCGAT"
gc = gc_content(dna_sequence)
print(gc)
# Output: 57.14 %