### Biology intro, Rosalind, DNA and proteins

```Bioinformatics
Prof. William Stafford Noble
Department of Genome Sciences
Department of Computer Science and Engineering
University of Washington
[email protected]
Outline
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Introductions
Biology background
Rosalind
Sequence alignment
Washington state
2,763 miles
Washington, DC
Scout
Jack
Nan
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:
1. I do not know this concept.
2. I have heard of this concept, but could not give a precise definition.
3. I know this concept well.
On the index card, write
1.
2.
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4.
5.
6.
The year and subject of your bachelors degree
advanced) in Python, linear algebra, statistics, and
biology
7. An interesting thing you have done
8. One question for me
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Name: Bill Noble
Email: [email protected]
Country: United States
Degree: 1991 Symbolic Systems
Favorite course: Programming Methodology
Biology: intermediate
Interesting thing I have done: unicycling
Question: …
Course goals
By the end of this course, you
should be able to
• Describe some basic
computational challenges in
bioinformatics.
• Implement and use several
basic algorithms in this
field.
algorithms.
This course will not
• Teach molecular biology
techniques.
• Teach you how to use offthe-shelf bioinformatics
software.
What is life?
• Entropy: the tendency toward disorder.
– Living organisms have low entropy.
– Soil has high entropy.
The cell
• Primary low entropy
compartment
– Gather energy
– Maintain inside/outside
distinction
• Strategies:
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Movement
Signal transduction
Energy capture
Reproduction
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
DNA
Transcription
lejeuneusa.org
RNA
Translation
Protein
Video
rcsb.org
4-letter DNA alphabet
• DNA consists of an
alphabet of four
bases
– Cytosine
– Guanine
– Thymine
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
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 complement
TCAGGTCACAGTT
|||||||||||||
AACTGTGACCTGA
Rosalind: Complementing a strand of DNA
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?