Wednesday, Jan 23rd

UCSD CSE 180

Yana Safonova

1. Give definitions of direct and reverse half-strands

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2. What are Okazaki fragments?

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3. Describe the role of the deamination process in DNA replication?

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4. Compute the ExtendedGenome for Genome = “AGCGATTTTGCTAGC”

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5. Compute SymbolArray for ExtendedGenome from the previous question and all nucleotides

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6. Describe FASTA format

Programming practice

• Python, command line interface

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• Basic structures and objects
• List
• String
• Set
• Dictionary

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• Manipulations with lists

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• Most common errors and how to deal with them

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List

• An ordered collection of elements
• my_list = []
• my_list = list()
• my_list = [1, 2, 3, 4, 5]
• my_list = [0] * 10
• Important functions (https://docs.python.org/2/tutorial/datastructures.html):
• append
• extend
• insert
• index
• remove
• count
• sorted(my_list)

List practice

• Create a list A with integers from 1 to 300 (including both values) and a list B with integers from 400 to 101 (including both values)
• Create a list C equals to [A[0], B[0], A[1], B[1], …, A[299], B[299]]
• Create a list D with integers from 100 to 200 (including both values)
• Find the second occurence of 200 in C and insert all values of D to C in front of it
• Sort C in both increasing and decreasing orders
• Output all integers appearing two or more times in C

String

• my_string = ‘Lorem ipsum dolor sit amet’
• my_string = “Lorem ipsum dolor sit amet”
• string is unchangeable!

my_string[0] # ERROR

• for c in my_string:

print c

• for i in range(len(my_string)):

print my_string[i]

• my_string.split()
• my_string.split(‘m’)

String

• my_string = ‘AAACGAAACGAAA’

pattern = ‘AAA’

for i in range(len(my_string)):

if my_string.find(pattern, i) != -1:

print i

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• my_string = my_string.replace(‘AAA’, ‘TTT’)
• my_string = my_string.lower()
• my_string = my_string.upper()

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https://docs.python.org/2.7/library/string.html

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