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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


Washington state

2,763 miles

Washington, DC


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


  • 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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