A Program to Transcribe a DNA Sequence into RNA

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A Program to Transcribe a DNA Sequence into RNA

• HI5100 Data Structures for BioInformatics
• Lesson 7

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OBJECTIVES

• In this lesson you will
• Develop an algorithm.
• Translate the algorithm into a Pytyon program.

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DNA Sequence Representation

• You can represent a DNA sequence as a string
• DNA is composed of the four nucleic acids
  (nucleotides, bases)
• Adenine A
• Cytosine C
• Guanine G
• Thymine T
• The single letters are standard IUB / IUPAC
  nucleic acid codes
• IUB (International Union of Biochemistry)
• IUPAC (International Union of Pure and Applied
  Chemistry http//www.iupac.org/index_to.html)

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DNA Sequence
ACCGATACGCCACTTAACAG
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DNA to RNA

• Very complex cellular mechanism
• Fairly simple from a programming standpoint
• Change all the Ts in the sequence to Us

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Understand the Problem Take 1

• From a computer processing perspective
• The computer must
• Examine each letter in the sequence
• Determine if it is a T
• If it is, replace it with a U

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Example
ACCGATACGCCACTTAACAG
First T is in position 5
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Example

• Can you replace the letter in position 5 with a
  different letter?

ACCGATACGCCACTTAACAG
U
First T was in position 5
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Try It
DNA_to_RNA.py def main() DNA1
ACCGATACGCCACTTAACAG print DNA1 DNA5
U print DNA1
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Results
Translation You cannot assign a value to one
item in a string sequence.
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Understand the Problem Take 2

• The computer must
• Examine each letter in the sequence
• Determine if it is a T
• If it is, create a new string with a copy of
  everything up to the T
• Concatentate a U
• Continue looking through the original string for
  more Ts

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Example
ACCGATACGCCACTTAACAG
ACCGA
U

• Continue looking in original string

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Build the Algorithm in Pseudocode
Set start_pos to 0 Find the position of the next
T Assign it to t_pos Copy characters from
start_pos to t_pos-1 into a new
string Concatenate a U Set start_pos to
t_pos1 Continue looking at characters in
original string Repeat from second line

• Think of the pseudocode as a rough draft of the
  final algorithm

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Or as a Flowchart P. 1
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Or as a Flowchart p. 2

• Think of the flowchart as a rough draft of the
  algorithm at this point

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Pseudocode / Flowchart

• Once you have the algorithm developed to a point
  where you can write some code, proceed with
• Write code
• Test
• Write code
• Test

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Assignment 2

• Use the psuedocode and flowchart drafts of the
  DNA to RNA algorithm to build a small program
  that
• Reads DNA sequences from a text file
• Converts each sequence into RNA
• Saves the RNA sequence to a text file
• Prints the DNA sequence on one line
• Directly underneath on the next line prints the
  RNA
• Continues reading, converting, writing to file,
  and printing until there is no more data in the
  text file

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Assignment 2

• A text file with several test strings is provided
  as DNAtest.csv
• Add data to DNAtest.csv so that all important
  special test cases are demonstrated, for example
• A sequence that starts with T
• A sequence that ends with T
• A sequence with no Ts
• A sequence that is all Ts

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Summary

• That covers computing with Python in a nutshell
• Now we are ready to tackle some data structures!

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End of Slides for Lesson 7

• HI5100 Data Structures for BioInformatics
• Lesson 7