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Bioinformatics. Prof. William Stafford Noble Department of Genome Sciences Department of Computer Science and Engineering University of Washington [email protected] Outline. Introductions Biology background Rosalind Sequence alignment. Washington state. 2,763 miles. Washington, DC.

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bioinformatics

Bioinformatics

Prof. William Stafford Noble

Department of Genome SciencesDepartment of Computer Science and Engineering

University of Washington

[email protected]

outline
Outline
  • Introductions
  • Biology background
  • Rosalind
  • Sequence alignment
slide3

Washington state

2,763 miles

Washington, DC

slide6

Scout

Nan

Jack

introductory survey
Introductory survey
  • p-value
  • t test
  • BLAST
  • Python sys.argv
  • support vector machine
  • false discovery rate
  • dynamic programming
  • recursion
  • hierarchical clustering
  • Wilcoxon test
  • Python tuple
  • Smith-Waterman
  • Bonferroni correction
  • Python dictionary

Next to each concept, please enter 1, 2 or 3, as follows:

I do not know this concept.

I have heard of this concept, but could not give a precise definition.

I know this concept well.

Do not sign your name.

on the index card write
On the index card, write
  • Your name
  • Your email address
  • Your home country
  • The year and subject of your bachelors degree
  • The name of your favorite undergraduate course
  • Your proficiency (introductory, intermediate, advanced) in Python, linear algebra, statistics, and biology
  • An interesting thing you have done
  • One question for me
slide10

Name: Bill Noble

  • Email: [email protected]
  • Country: United States
  • Degree: 1991 Symbolic Systems
  • Favorite course: Programming Methodology
  • Python: advanced
  • Statistics: advanced
  • Biology: intermediate
  • Interesting thing I have done: unicycling
  • Question: …
course goals
Course goals

By the end of this course, you should be able to

This course will not

Teach molecular biology techniques.

Teach you how to use off-the-shelf bioinformatics software.

  • Describe some basic computational challenges in bioinformatics.
  • Implement and use several basic algorithms in this field.
  • Describe several advanced algorithms.
what is life
What is life?
  • Entropy: the tendency toward disorder.
    • Living organisms have low entropy.
    • Soil has high entropy.
the cell
The cell
  • Primary low entropy compartment
  • Tasks:
    • Gather energy
    • Maintain inside/outside distinction
  • Strategies:
    • Movement
    • Signal transduction
    • Energy capture
    • Reproduction
biological macromolecules
Biological macromolecules
  • Lipids (fat):
    • membranes
    • energy storage
  • Carbohydrates (sugar):
    • energy storage
    • structure
    • cell-cell communication
  • Nucleic aids
    • genetic material
  • Proteins
    • workhorses of the cell
the central dogma of molecular biology
The central dogma of molecular biology

DNA

Transcription

RNA

lejeuneusa.org

Translation

Protein

Video

rcsb.org

4 letter dna alphabet
4-letter DNA alphabet
  • DNA consists of an alphabet of four bases
    • Adenine
    • Cytosine
    • Guanine
    • Thymine
rosalind
Rosalind
  • Visit http://rosalind.info and create a login.
  • Enroll in this class via http://rosalind.info/classes/enroll/e7948c7e32/
  • Solve the problem, “Installing Python”
  • Solve the problem, “Counting DNA nucleotides.”
reverse complement
Reverse complement

T

C

TCAGG

TCAGGTCACAGTT

A

Write down the rest of the DNA sequence.

G

G

AAC

AACTGTGACCTGA

Write down the sequence you get by reading from the blue strand, starting at the bottom.

reverse complement1
Reverse complement

TCAGGTCACAGTT

|||||||||||||

AACTGTGACCTGA

Rosalind: Complementing a strand of DNA

one minute response
One-minute response

At the end of each class

  • Write for about one minute.
  • Provide feedback about the class.
  • Was part of the lecture unclear?
  • What did you like about the class?
  • Do you have unanswered questions?
  • Sign your name

I will begin the next class by responding to the one-minute responses

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