Difference between revisions of "Python for Biologists/C2/Introduction-to-Python-for-Biologists/English"

Revision as of 18:49, 12 August 2014

Title of script: Introduction to Python for Biologists

Author: Trupti Rajesh Kini & Snehalatha

Keywords: video tutorial, Python, DNA seqences, Protein sequences, Biologists

Visual Cue	Narration
Slide 1	Welcome to the spoken-tutorial on Introduction to Python for Biologists.
Slide 2 Learning Objectives	In this tutorial we will learn, Installation of Python/IPython interpreter. Simple Python programs using examples of DNA and Protein sequences.
Slide 3 System Requirements	To record this tutorial, I am using Ubuntu OS version 12.04 Python 3.2.3 IPython 0.12.1
Slide 4 Prerequisites	To practice this tutorial you should be familiar with, Basic biochemistry You can also refer to Spoken Tutorials on Python for better understanding of this tutorial. These are available at www.spoken-tutorial.org
Slide 5 Why Python for biologists?	Some of the features of Python useful for biologists are as follows: Python has many tools to write small programs that are useful in biology. It has a consistent syntax. It has built-in-libraries for common tasks. We can manipulate DNA and protein sequences easily .
Slide 6 Why Pyhton for biologists?	* It has a large user base as it is commonly used in bioinformatics. Listed here are examples of few bioinformatic tools in Python: Biopython, Modeller, chemopy, BLASTorage, Pymol For more information, refer the given website : http://pythonforbiologists.com
Slide 7 Installation	* Python comes installed, by default on Ubuntu. IPython is an interactive terminal for Python To install Python on Windows, Mac OS and Android devices, visit the given link www.python.org
Open terminal by pressing Ctrl+Alt+T at the same time.	Open the terminal by pressing Ctrl+Alt+T simultaneously. Python comes installed, by default on Ubuntu.
Type sudo apt-get install ipython3 and press Enter.	In case you don't, then manually install the latest version of IPython, by typing sudo apt-get install ipython3 and press Enter. Give root password if asked.
Cursor on the terminal.	Wait for a few minutes for the installation to complete. Note : Python3 does not overwrite the default Python on the system
Open the terminal Type ipython3 and press Enter.	To check whether ipython3 is installed successfully on your system, Type ipython3 and press Enter.
Cursor on the terminal Highlight the prompt	You will see few lines of information on Python like, the version number etc. You will also see the Ipython prompt on the terminal. Prompt indicates that Ipython is installed successfully.
Cursor on terminal	Let's type a few simple Python commands with an example of a DNA sequence.
Cursor on terminal	To begin with, we will store data, i.e DNA sequence in a variable called my_DNA.
Slide 8 What is a string?	In Python language, data such as protein and DNA sequences are called as strings. A string is a data in the form of a text.
Type in the terminal, my_DNA = "ATGCGCAT" Highlight my_DNA Press Enter	Let us go back to the terminal. Type, my_DNA is equal to within double quotes ATGCGCAT.Press Enter.
Highlight my_DNA	We call this as assigning a variable.
Highlight my_DNA	For writing a code, we can use the variable name instead of the string itself.
Type, print(my_DNA) and press Enter	To print the DNA sequence, we will use print function. For that type, print(my_DNA) and press Enter.
Highlight the output, ATGCGCAT	We get the sequence as output.
Cursor on the terminal.	Now let us print the sequence on two separate lines.
Press up arrow Add \n and DNA after ATGCGCAT . my_DNA = "ATGCGCAT\nDNA" Press Enter	Press up arrow on the key board till we get this command on the terminal. my_DNA = "ATGCGCAT” Lets edit this line. Type \n and DNA after the sequence within double quotes. Press Enter.
Type, print(my_DNA) and press Enter	Type, print(my_DNA) and press Enter.
Highlight the output ATGCGCAT DNA	The output prints the sequence on two separate lines ,
Slide 9 Assignment	As an assignment, Using example of a short proteinsequence given Print the sequence on a single line, and print the sequence on two separate lines.
Cursor on the terminal	Let us now learn a few more functions and methods.
Slide 10	Another useful built-in tool in Python is the len function. It is used to calculate the length of a string.
Let us go back to the terminal. Press up arrow key my_DNA = "ATGCGCAT" Press Enter	Let us go back to the terminal. Press up arrow on the key board till we get this command on the terminal. my_DNA = "ATGCGCAT” Press Enter
Type: len(my_DNA)	To find the length of the DNA sequence in a variable, type, len within brackets my_DNA Press Enter.
Cursor on the terminal	The output on the screen shows the number 8. This is the length of the DNA sequence stored in the variable my_DNA.
Slide 10 Assignment	Another assignment for you Calculate the length of the given DNA sequence `ATGGCATGCGC' and Store the output in a variable.
Slide 11	Many times in biochemistry, sequences are represented either in lowercase or uppercase alphabets.
Type, my_DNA=”ATGCGCAT” Press Enter Type my_DNA.lower() Press Enter.	To convert the uppercase alphabets in a string to lowercase: We make use of lower() method. Let us go back to the terminal. Type, my_DNA=”ATGCGCAT”. Press Enter Then type, my_DNA.lower(). In a method, we write, The name of the variable first, followed by a period(.), then the name of the method then we open and close parentheses. Press Enter.
Highlight 'atgcgcat'	The output shows the string in lowercase.
Slide 12 Assignment	As an assignment, Using example of a short protein sequence given Convert the sequence to uppercase. Hint: Use upper() method.
	Let us go back to terminal again
Type my_protein = `"alspadkanl"`	Lets take an example of an amino acid sequence. Store it in a variable called my_protein my_protein = `"alspadkanl"`
Slide 13	To find out the number of times an amino acid or a sequence of amino acids occurs in a string. We make use of count function
Type my_protein.count ('a') Press Enter	Let us go back to the terminal. For example to know the number of times amino acid Alanine occurs in the string Type my_protein.count ('a') Press Enter
Highlight 3	`Output shows number 3.` `There are 3 Alanines in the string.`
Type my_protein.count('l') Press Enter	Similarly to find number of Leucines in the string Type my_protein.count('l') Press Enter
Highlight 2	We get an output as 2, there are 2 Leucines in the string.
Cursor on the terminal	Similarly we can use DNA or an RNA sequence as string to count the ocurrences of basepairs .
Slide 12 Summary	Let us summarize, In this tutorial we learnt: Installation of IPython Interpreter Storing data in variables using examples of DNA and Protein sequences. Printing a sequence in single and on two separate lines
Slide 13 Summary	* Find the length of the string Change case of the string Count the number of times a character appears in a string
Slide 13 Assignment	Here is an assignment, Calculate GC content in the given DNA sequence. 'ATGGCATGCGC'
Slide 14 About Spoken Tutorial Project	The video available at the following link summarizes the Spoken Tutorial project. Pls watch it.
Slide 15 About Spoken Tutorial workshops	The Spoken Tutorial Project Team conducts workshops and gives certificates to those who pass an online test. For more details, please write to us.
Slide 16 Acknowledgement	Spoken Tutorial ProjecThese 3 slides remain as before, on LaTeX. Only the narration will now be as given here.t is supported by the NMEICT, MHRD, Government of India. More information on this Mission is available at this link.
	This script is contributed by Snehalatha and Trupti Kini. And this is Trupti Kini from IIT Bombay signing off. Thanks for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak, Trupti

Difference between revisions of "Python for Biologists/C2/Introduction-to-Python-for-Biologists/English"

Revision as of 18:49, 12 August 2014

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@@ Line 1: / Line 1: @@
-'''Title of script''': '''Introduction to Python for Biologists'''
+'''Title of script: Introduction to Python for Biologists '''
 '''Author: Trupti Rajesh Kini & Snehalatha '''
 '''Keywords: video tutorial, Python, DNA seqences, Protein sequences, Biologists'''
 {| style="border-spacing:0;"
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Visual Cue'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Visual Cue'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Narration'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Narration'''
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 1'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 1'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Welcome to the '''spoken-tutorial '''on''' Introduction to Python for Biologists.'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Welcome to the '''spoken-tutorial '''on '''Introduction to Python for Biologists.'''
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 2'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 2'''
 '''Learning Objectives '''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| In this tutorial we will learn,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| In this tutorial we will learn,
-* Installation of '''Python/IPython interpreter.'''
-* Simple '''Python''' programs using examples of''' DNA''' and Protein sequences.<br/>
+* Installation of '''Python/IPython interpreter.'''
+* Simple '''Python''' programs using examples of '''DNA''' and Protein sequences.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 3'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 3'''
 '''System Requirements'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| To record this tutorial, I am using
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To record this tutorial, I am using
 * '''Ubuntu OS version 12.04'''
 * '''Python 3.2.3'''
 * '''IPython 0.12.1'''
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 4'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 4'''
 '''Prerequisites'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| To practice this tutorial you should be familiar with,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To practice this tutorial you should be familiar with,
 * Basic biochemistry
 You can also refer to '''Spoken Tutorials''' on '''Python''' for better understanding of this tutorial.
+These are available at '''www.spoken-tutorial.org'''
-These are available at '''www.spoken-tutorial.org'''
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 5'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 5'''
 '''Why Python for biologists?'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Some of the features of '''Python''' useful for biologists are as follows:
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Some of the features of '''Python''' useful for biologists are as follows:
+* Python has many tools to write small programs that are useful in biology.
-* Python has many tools to write small <br/> programs that are useful in biology.
+* It has a consistent syntax.
-* It has a consistent syntax.
+* It has built-in-libraries for common tasks.
-* It has built-in-libraries for common tasks.
+* We can manipulate DNA and protein sequences easily .
-* We can manipulate DNA and protein sequences easily .
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 6 '''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 6 '''
-'''Why Pyhton for biologists?'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"|
-* It has a large user base as it is commonly used in bioinformatics.
-* Listed here are examples of few bioinformatic tools in Python:
-'''Biopython, Modeller, chemopy, BLASTorage, Pymol'''
+'''Why Pyhton for biologists?'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| * It has a large user base as it is commonly used in bioinformatics.
+* Listed here are examples of few bioinformatic tools in Python:
+'''Biopython, Modeller, chemopy, BLASTorage, Pymol'''
-For more information, refer the following website :
+For more information, refer the given website&nbsp;:
-'''http://pythonforbiologists.com'''
+[http://pythonforbiologists.com/ http://pythonforbiologists.com]
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 7'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 7'''
 '''Installation'''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"|
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| * '''Python''' comes installed, by default on Ubuntu.
-* '''Python comes installed by default on Ubuntu.'''
+* IPython is an interactive terminal for Python
-* IPython is an interactive terminal for Python
+* To install '''Python '''on '''Windows, Mac OS '''and '''Android '''devices, visit the given link<br/> '''www.python.org'''
-* To install '''Python '''on '''Windows, Mac OS '''and '''Android '''devices, visit '''www.python.org'''
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Open terminal by pressing Ctrl+Alt+T at the same time.
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Open terminal by pressing '''Ctrl+Alt+T''' at the same time.
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"|
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Open the terminal by pressing '''Ctrl+Alt+T''' simultaneously.
-Open the '''terminal by pressing '''Ctrl+Alt+T''' simultaneously.
-Python comes installed by default on Ubuntu.
+Python comes installed, by default on Ubuntu.
-In case you don't, then manually install the latest version of '''IPython''',
-By typing
-'''sudo apt-get install ipython3'''
-and press '''Enter.'''
-Give root password if asked.
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type '''sudo apt-get install ipython3'''
-'''sudo apt-get install ipython3'''
+and press '''Enter.'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| In case you don't, then manually install the latest version of '''IPython''', by typing
-and press '''Enter.'''
+'''sudo apt-get install ipython3'''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"|
-In case you don't, then manually install the latest version of '''IPython''',
+and press '''Enter.'''
-By typing
-'''sudo apt-get install ipython3'''
+Give root password if asked.
-and press '''Enter.'''
-Give root password if asked.
+|-
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal.
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Wait for a few minutes for the installation to complete.
+Note : '''Python3''' does not overwrite the default Python on the system
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Open the terminal
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Wait for a few minutes for the installation to complete.
-Note:Python3 does not overwrite the default Python on the system
-|-
+Type '''ipython3''' and press '''Enter.'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Open the terminal
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To check whether '''ipython3''' is installed successfully on your system,
-Type''' ipython3''' and press '''Enter.'''
+Type '''ipython3 '''and press '''Enter.'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| To check whether '''ipython3''' is installed successfully on your system,
-Type''' ipython3 ''' and press '''Enter.'''
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
+Highlight the prompt
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| You will see few lines of information on '''Python '''like, the version number etc.
-Point to “>>>” symbol.
+You will also see the '''Ipython '''prompt on the''' '''terminal'''.'''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| You will see few lines of information on '''Python '''like, the version number.
-You will also see the '''IPython''' prompt on the terminal.
+Prompt indicates that '''Ipython '''is installed successfully.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on terminal
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on terminal
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Let's type a few simple '''Python''' commands with an example of a '''DNA '''sequence.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let's type a few simple '''Python''' commands with an example of a '''DNA '''sequence.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on terminal
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on terminal
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| To begin with, we will store data, i.e '''DNA sequence '''in a variable called '''my_DNA.'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To begin with, we will store data, i.e '''DNA sequence '''in a variable called '''my_DNA.'''
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 8'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 8'''
-'''What is a string?'''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| In '''Python''' language, data such as '''protein''' and '''DNA''' sequences are called as '''strings'''.
+'''What is a string?'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| In '''Python''' language, data such as '''protein''' and '''DNA''' sequences are called as '''strings'''.
 A '''string''' is a data in the form of a text.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type in the terminal,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type in the terminal,
 '''my_DNA = "ATGCGCAT"'''
 Highlight '''my_DNA'''
 Press '''Enter'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us go back to the terminal.
-'''my_DNA equal to ATGCGCAT '''within double quotes
+Type,
+'''my_DNA is equal to within double quotes ATGCGCAT.'''Press '''Enter'''.
-Press '''Enter'''.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the panel.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight '''my_DNA'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| We call this as '''''assigning''''' a variable.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| We call this as '''''assigning''''' a variable.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the panel
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight '''my_DNA'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| For writing a code, we can use the variable name instead of the string itself.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| For writing a code, we can use the variable name instead of the string itself.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type,
-'''my_DNA '''and press '''Enter'''
+'''print(my_DNA) '''and press '''Enter'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| To print this sequence, type
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To print the DNA sequence,
-'''my_DNA '''and press '''Enter.'''
+we will use '''print '''function.
+For that type,
+'''print(my_DNA) '''and press '''Enter.'''
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight the output,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight the output,
 '''ATGCGCAT'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| This will print the '''DNA '''sequence, '''ATGCGCAT '''within single quotes as it is a string.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| We get the sequence as output.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal.
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Now let us print the sequence on two separate lines.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Now let us print the sequence on two separate lines.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Press '''up '''arrow
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Press '''up '''arrow
 Add '''\n '''and '''DNA '''after '''ATGCGCAT''' '''.'''
 '''my_DNA = "ATGCGCAT\nDNA"'''
 Press '''Enter'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Press '''up '''arrow on the key board till we get this command on the '''terminal.'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Press '''up '''arrow on the key board till we get this command on the '''terminal.'''
 '''my_DNA = "ATGCGCAT” '''
 Lets edit this line.
-Type '''\n '''and '''DNA '''after '''ATGCGCAT '''within double quotes.
+Type '''\n '''and '''DNA '''after the sequence''' '''within double quotes.
 Press '''Enter.'''
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type,
 '''print(my_DNA) '''and press '''Enter'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type,
 '''print(my_DNA) '''and press '''Enter.'''
@@ Line 249: / Line 227: @@
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight the output
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight the output
 '''ATGCGCAT'''
 '''DNA'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| The output prints the sequence on two separate lines as,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| The output prints the sequence on two separate lines ,
-'''ATGCGCAT'''
-'''DNA'''
-<nowiki><<PAUSE>></nowiki>
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 9'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 9'''
 '''Assignment'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| As an assignment,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| As an assignment,
-* Using example of a short protein<br/> sequence: '''CNLTFTWPEADFYPI Protein'''<br/>
+* Using example of a short proteinsequence given
+* Print the sequence on a single line, and print the sequence on two separate lines.
-* Print the above sequence on a single line, and also on two separate lines.
-<nowiki><<PAUSE>></nowiki>
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Let's go back to the '''terminal '''and learn a few more '''functions '''and '''methods'''.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us now learn a few more '''functions '''and '''methods'''.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"|
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Slide 10
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Another useful built-in tool in '''Python''' is the '''len''' '''function'''.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Another useful built-in tool in '''Python''' is the '''len''' '''function'''.
+It is used to calculate the length of a string.
-It is used to calculate the length of a string.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Press up arrow key
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us go back to the terminal.
-'''my_DNA = "ATGCGCAT"'''
+Press up arrow key
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Press '''up '''arrow on the key board till we get this command on the '''terminal.'''
-'''my_DNA = "ATGCGCAT”'''
+'''my_DNA = "ATGCGCAT"'''
 Press '''Enter'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us go back to the terminal.
+Press '''up '''arrow on the key board till we get this command on the '''terminal.'''
+'''my_DNA = "ATGCGCAT”'''
+Press '''Enter'''
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type:
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type:
 len(my_DNA)
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| To find the length of the '''DNA''' sequence in a variable, type,
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To find the length of the '''DNA''' sequence in a variable, type,
-'''len '''within brackets '''my_DNA'''
+'''len '''within brackets '''my_DNA'''
 Press '''Enter.'''
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| The output on the screen shows the number 8.
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| The output on the screen shows the number 8.
+This is the length of the '''DNA '''sequence stored in the variable '''my_DNA.'''
-This is the length of the '''DNA '''sequence stored in the variable '''my_DNA.'''
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 10'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 10'''
+'''Assignment'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Another assignment for you
-'''Assignment'''
+* Calculate the length of the given '''DNA '''sequence `ATGGCATGCGC'
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Another assignment for you
-* Calculate the length of the given '''DNA '''sequence `ATGGCATGCGC'<br/>
+* and Store the output in a variable.
-* Store the output in a variable.
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"|
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Slide 11
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Lets go back to the terminal
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Many times in biochemistry, sequences are represented either in &nbsp;lowercase or uppercase &nbsp;alphabets.
-|-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"|
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Many times in biochemistry, sequences are represented either in &nbsp;lowercase or uppercase &nbsp;alphabets.
@@ Line 339: / Line 311: @@
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type '''protein =” ”'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type,
-Press '''Enter'''
+'''my_DNA=”ATGCGCAT”'''
-Type '''my_DNA'''.'''lower()'''
+Press '''Enter'''
-Press '''Enter.'''
+Type '''my_DNA'''.'''lower()'''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| To convert the uppercase alphabets in a string to &nbsp;lowercase:
-We make use of '''lower()''' method.
+Press '''Enter.'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To convert the uppercase alphabets in a string to &nbsp;lowercase:
-Type,
+We make use of '''lower()''' method.
-'''my_DNA=”ATGCGCAT”. &nbsp;'''Press '''Enter'''
+Let us go back to the terminal.
-Then type, '''my_DNA'''.'''lower().'''
+Type,
-In a method, we write,
+'''my_DNA=”ATGCGCAT”. &nbsp;'''Press '''Enter'''
-* The name of the variable first,
+Then type, '''my_DNA'''.'''lower().'''
-* followed by a period(.),
-* then the name of the method
-* then we open and close parentheses.
-Press '''Enter.'''
+In a method, we write,
+* The name of the variable first,
+* followed by a period(.),
+* then the name of the method
+* then we open and close parentheses.
+Press '''Enter.'''
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight &nbsp;''''atgcgcat''''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight &nbsp;''''atgcgcat''''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| The output shows the string in lowercase.
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| The output shows the string in lowercase.
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 11'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 12'''
 '''Assignment'''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| As an assignment,
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| As an assignment,
 Using example of a short protein
-sequence: &nbsp;'''cnltftwpeadfypi'''
+sequence given
 Convert the sequence to uppercase'''.'''
 '''Hint: Use upper() method.'''
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"|
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"|
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Back to terminal again
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us go back to terminal again
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type
 my_protein = <tt>"alspadkanl"</tt>
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Lets take an example of an amino acid sequence.
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Lets take an example of an amino acid sequence.
-Store it in a variable called protein
+Store it in a variable called '''my_protein'''
 my_protein = <tt>"alspadkanl"</tt>
@@ Line 401: / Line 377: @@
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Slide 13
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| To find out the number of times an amino acid or a sequence of amino acids occurs in a string.
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To find out the number of times an amino acid or a sequence of amino acids occurs in a string.
 We make use of '''count '''function
@@ Line 410: / Line 386: @@
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type
 my_protein.count ('a')
+Press '''Enter'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us go back to the terminal.
-Press enter
+For example to know the number of times amino acid '''Alanine''' occurs in the string
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| For example to know the number of times amino acid Alanine occurs in the string
 Type
 my_protein.count ('a')
+Press '''Enter'''
-Press enter
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight 3
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| <tt>Output shows number 3.</tt>
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| <tt>Output shows number 3.</tt>
-<tt>There are 3 Alanines in the string. </tt>
+<tt>There are 3 '''Alanines''' in the string. </tt>
@@ Line 436: / Line 411: @@
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Type
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type
 my_protein.count('l')
-Press enter
+Press '''Enter'''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Similarly to find number of Leucines in the string
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Similarly to find number of''' Leucines''' in the string
 Type
 my_protein.count('l')
-Press enter
+Press '''Enter'''
@@ Line 453: / Line 428: @@
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight 2
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| We get an output as 2, there are 2 Leucines in the string.
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| We get an output as '''2''', there are '''2''' '''Leucines''' in the string.
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on the terminal
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Similarly we can use DNA or an RNA sequence as string to count the ocurrences of basepairs .
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Similarly we can use DNA or an RNA sequence as string to count the ocurrences of basepairs .
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 12'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 12'''
 '''Summary'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us summarize,
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us summarize,
-In this tutorial we have learnt:
+In this tutorial we learnt:
+* Installation of '''IPython Interpreter'''
-* Installation of '''IPython Interpreter'''
+* Storing data in variables using
-* Storing data in variables using
 examples of '''DNA''' and '''Protein'''
 sequences.
 * Printing a sequence in single and on two separate lines
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 13'''
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 13'''
 '''Summary'''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| * Find the length of the string
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| * Find the length of the string
-* Change case of the string <br/>
-* Count the number of times a character appears in a string
+* Change case of the string
+* Count the number of times a character appears in a string
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Slide 13
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Slide 13
 '''Assignment'''
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Here is an assignment,
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Here is an assignment,
 Calculate GC content in the given DNA sequence.
 'ATGGCATGCGC'
@@ Line 510: / Line 485: @@
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 14'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 14'''
 '''About Spoken Tutorial Project'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| The video available at the following link summarizes the Spoken Tutorial project. Pls watch it.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| The video available at the following link summarizes the Spoken Tutorial project. Pls watch it.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 15'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 15'''
-'''About Spoken Tutorial workshops'''
+'''About Spoken Tutorial workshops'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| The Spoken Tutorial Project Team conducts workshops and gives certificates to those who pass an online test.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| The Spoken Tutorial Project Team conducts workshops and gives certificates to those who pass an online test.
 For more details, please write to us.
 |-
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 16'''
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 16'''
 '''Acknowledgement'''
-| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| Spoken Tutorial ProjecThese 3 slides remain as before, on LaTeX. Only the narration will now be as given here.t is supported by the NMEICT, MHRD, Government of India.
+| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Spoken Tutorial ProjecThese 3 slides remain as before, on LaTeX. Only the narration will now be as given here.t is supported by the NMEICT, MHRD, Government of India.
 More information on this Mission is available at this link.
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"|
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"|
-| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0cm;padding-left:0.191cm;padding-right:0.191cm;"| This script is contributed by Snehalatha and Trupti Kini.
+| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| This script is contributed by Snehalatha and Trupti Kini.
-And this is Trupti Kini from''' IIT Bombay''' signing off.
+And this is Trupti Kini from '''IIT Bombay''' signing off.
 Thanks for joining.
 |}