🧬 Lecture 2: DNA Analysis & Sequence Processing

Interactive notebooks for string manipulation, conditionals, dictionaries, debugging, and working with FASTA files.

🎯 Getting Started

Start with String Manipulation - Learn the fundamentals of working with DNA sequences.

Master conditionals and dictionaries - Essential tools for biological programming.

Real biological problems - Work with actual DNA sequences and FASTA files.

Available

🧬 String Manipulation for DNA

Master string slicing and loops to analyze DNA sequences

  • ▸String slicing with [start:end] notation
  • ▸Extracting subsequences from DNA
  • ▸Looping through string positions
  • ▸Finding patterns in sequences
  • ▸Hands-on DNA manipulation exercises
Open in Colab
Available

🎯 Python Conditionals

Learn to make decisions in code with if/elif/else statements

  • ▸If statements and boolean logic
  • ▸Comparing sequences with ==
  • ▸Finding start and stop codons
  • ▸Elif for multiple conditions
  • ▸Combining loops and conditionals
Open in Colab
Available

📊 Dictionaries & Translation

Use dictionaries to translate DNA to protein sequences

  • ▸Python dictionaries for genetic code
  • ▸Key-value pairs for codon mapping
  • ▸Translating DNA to amino acids
  • ▸Handling special codons
  • ▸Building protein sequences
Open in Colab
Available

🐛 Debugging Biological Code

Learn to identify and fix common errors in biological programming

  • ▸Syntax errors in biological code
  • ▸Type errors with biological data
  • ▸Name errors and undefined variables
  • ▸Logic errors in calculations
  • ▸Debugging strategies and tips
Open in Colab
Available

📁 Working with FASTA Files

Read and process real biological sequence files

  • ▸Understanding FASTA format
  • ▸Reading sequences from files
  • ▸Parsing headers and sequences
  • ▸Processing multiple sequences
  • ▸Writing results to files
Open in Colab
Apply It!

🧬 DNA Analysis Toolkit

Real Python tools for DNA sequence analysis!

  • ▸GC content calculator
  • ▸Reverse complement generator
  • ▸ORF finder and translator
  • ▸Codon usage analyzer
  • ▸Restriction site mapper
Open in Colab

🗺️ Learning Path

Fundamentals: String manipulation and conditionals

Data Structures: Dictionaries for genetic code

Debugging: Finding and fixing code errors

File Handling: Working with FASTA files

🎓 Skills You'll Master

By completing these notebooks, you'll be able to:

  • ✓Manipulate DNA sequences using string slicing
  • ✓Use conditionals to make decisions in code
  • ✓Work with dictionaries for genetic code translation
  • ✓Debug common programming errors effectively
  • ✓Read and process FASTA sequence files
  • ✓Build robust biological data analysis scripts

📚 Part of the Python for Biologists course by Helfrid Hochegger

University of Sussex | Year 3 Biology, Biochemistry & Neuroscience