bioinformatics

• Bioinformatics


  Using computer technology to collect, store, analyse and disseminate biological data and information
• $100 million/ genome


  2003
• $100/genome


  2023
• These bioinformatics skills are becoming important in the job market
• Analysis range


  • Genes
  • Systems biology
• Uses of bioinformatics


  • Genome sequence and annotation
  • Protein structure and molecular binding
  • DNA identification
  • Omics studies (large-scale study of various biomolecules)
• Common problems with bioinformatics

  • Large number of tools available
  • Not very user friendly
  • Outputs look intimidating
  • Different file formats
• Food detective


  2013 horsemeat scandal where horse and pig DNA were found in beef dishes
• DNA barcoding

  Allows species identification through short section of DNA (amplified by PCR)
• Uses of DNA barcoding

  • Food fraud detection
  • Identifying pollens
  • Pathogen surveillance
• FASTA format


  Starts with definition line, optional description, then the sequence
• GenBank


  File format has a lot more information
• Getting DNA data


  1. Template DNA made into smaller pieces

  2. DNA fragments

  3. Sequencer

  4. Read
• Starfish species identification


  DNA barcoding can be used to build Phylogenetic trees where length of line indicates how many changes there have been to the DNA
• Clade


  A group of organisms that include a single ancestor and all of its descendants
• Outgroup


  Quite different to the other samples to be able to find distances from other groups and group them
• CLUSTAL


  Type of alignment file
• Query


  Asking database for a piece of data
• Primary key


  Unique ID for identifying an entry in a table in a database
• Gene Cards


  Human gene database with extensive information on each gene
• PDB (protein data base) format


  Used to store information on protein structure