Workshop 1 Background Slides

Ancient DNA: Key Concepts

• Ancient DNA (aDNA) is often fragmented and chemically damaged
• Mitochondrial genomes are commonly used due to their abundance and small size
• Public resources: Allen Ancient DNA Resource (AADR), NCBI GenBank

Downloading Genomic Data

• Most public databases provide FASTA files for genome sequences
• Data can be downloaded via web browser, curl, wget, or programmatically (e.g., Python requests)
• Always check data licensing and usage restrictions

FASTA File Format

• Text-based format for nucleotide or protein sequences
• Begins with a “>” header line, followed by sequence lines
• Example:

  >Sample1 mtDNA
  ATGCGT...
  

Calculating Sequence Statistics

• Sequence length: Number of nucleotides
• GC content: Percentage of G and C bases
• Useful for quality checks and basic characterization
• Can be computed with simple Python scripts

Using LLMs for Bioinformatics

• LLMs can help write, debug, and improve code
• Effective prompts are clear, specific, and goal-oriented
• Always verify outputs and iterate as needed