1. Intro

Question 1

Terms and concepts
* prerequisites - molecular genetics - principles of Sanger sequencing, next generation sequencing
* sequence assembly
* Margaret Dayhoff & her contributions
* examples of applications of sequencing data in biology
* linux: connect to the cluster using ssh

Question 2

Explain Sanger sequencing

Question 3

Explain Illumina sequencing

Question 4

Explain PacBio sequencing

Question 5

Protein Sequencing?

Answer 5

Deducing (assembling) the target sequence

data: protein sequence fragments (eg breakdown P and breakdown Q of same protein)

approach: test all possible combinations for overlap between P and Q fragments

Question 6

Name two early Bioinformaticians and their background

Answer 6

Margaret Dayhoff and Walter Goad (physicists and statisticians)

• became interested in biological data
• imported tools & problems & practices into biology

biological sequences: fundamental in biology
* became increasingly available in the 1950s
* one dimension, patterns of symbols:amenable to quantitative & computational tools

Question 7

Early sequence bioinformatics ?

Answer 7

1. data storage and management
   * centralizing of data
   * sequence database
2. sequence analysis ➟ mathematical problems:
   * pattern matching and detecting
   - assemble sequences, analyze conserved sequence patterns, identify homologs
   * statistical problems
   - codon bias
   * “paleogenetics”: use sequences to document
   evolutionary history of sequences & organisms