Biopython/C2/Manipulating-Sequences/English

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Manipulating Sequences.
Slide Number 2 Learning Objectives	In this tutorial, we will use Biopython tools to; 1. Generate a random DNA sequence . 2. Slice a DNA sequence at specified locations. 3. Join two sequences together to form a new sequence that is to Concatenate.
Slide Number 3 Learning Objectives (Biopython Functions)	4. Find the length of the sequence. 5. Count the number of individual bases or part of the string. 6. Find a particular base or part of the string. 7. Convert a sequence object to a mutable sequence object.
Slide Number 4 Pre-requisites	To follow this tutorial you should be familiar with, Undergraduate Biochemistry or Bioinformatics And Basic Python programming If not: Refer to the Python tutorials at the given link.
Slide Number 5 System Requirement	To record this tutorial I am using, Ubuntu OS version. 14.10 Python version 2.7.8 Ipython interpretor version 2.3.0 Biopython version 1.64
Press ctrl, alt and t simultaneously. At the prompt, type ipython.	Let me open the terminal and start ipython interpretor. Press ctrl, alt and t keys simultaneously. At the prompt, type ipython and press enter. Ipython prompt appears on the screen.
Generating random DNA sequence in python	Using Biopython we can generate a sequence object for a random DNA sequence of any specified length. Let us now generate a sequence object for a DNA sequence of 20 bases. At the prompt. Type import random Press enter
Fr At the prompt type from Bio.Seq import Seq	Next import Seq module from Bio package. Often Seq is pronounced as seek.
Type, from Bio.Seq import Seq Press Enter	At the prompt type, From Bio dot Seq import Seq (from Bio.Seq import Seq ) Press Enter
Cursor on the terminal.	We will use Bio.Alphabet module to specify the alphabets in the DNA sequence.
Type, >>>from Bio.Alphabet import generic_dna	Type, from Bio dot alphabet import generic underscore dna. (from Bio.Alphabet import generic_dna) Press enter
Type, dna1 = Seq( .join(random.choice('AGTC') for _ in range(30)),generic_dna) Press enter	Type the following command to create a sequence object for the random DNA sequence; Store the sequence in a variable dna1 Please note in this command use two single quotes instead of a double quote. Press enter.
type >>> dna1 Press enter	For the output, type dna1. Press enter
Highlight output.	The output shows the sequence object for the random DNA sequence.
Cursor on the terminal. Press up arrow key Press enter. type >>> dna1 Press enter	If you want a new sequence, press up arrow key to get the same command as above. Press enter. For the output, type the variable name, dna1. Press enter
Cursor on the terminal.	The output shows a new DNA sequence, which is different from the first one.
Slide number 6and 7 Sequence Objects	About Sequence Objects The sequence objects usually act like normal Python strings. So follow the normal conventions as you do for Python strings In Python,We count the characters in the string starting from 0 instead of 1. The first character in the sequence is position zero.
Cursor on the terminal. At the prompt type, string1 = my_seq[0:6] Highlight the first string from 1-5th character.	Back to the terminal. Often you many need to work with only a part of the sequence. Now lets see how to extract parts of the string and store them as sequence objects. For example we will slice the DNA sequence at two positions. First between bases 6 and 7. This will extract a fragment from the beginning of the sequence to the 6th base in the sequence.
Highlight the second string from 18th -30th character.	The second slice will be between bases 11 and 12. The second fragment will be from the 12th base to the end of the sequence.
At the prompt type,	Type the following command at the prompt to extract the first fragment. String1 equal to dna1 within brackets 0 semicolon 6. (string1 = dna1[0:6] ) string1 is the variable to store the first fragment. The rest of the command follows as in normal Python. Enclosed in these brackets are the start and stop positions separated by a colon. The positions are inclusive of the start, but exclusive of the stop position. Press Enter
Type, string1 press enter	To view the output Type, string1,press enter. The output shows the first fragment as the sequence object.
Type string2 = my_seq[11:20] press enter	To extract the second string from the sequence, Press up arrow key and edit the command as follows: Change the name of the variable to string2, and positions to 11 and 20.
Type string2 press enter.	For the output Type string2 press enter. Now we have the 2nd fragment also as a sequence object.
Type dna2 = string1 + string2 press enter	Let us concatenate, that is, add the two strings together to form a new fragment: Store the new sequence in a variable dna2. Type, dna2 equal to string1 plus string2 (dna2 = string1 + string2) press enter Please note; we can not add sequences with incompatible alphabets. That is we can not concatenate a DNA sequence and a protein sequence, to form a new sequence. The two sequences must have the same alphabet attribute.
Type dna2 Press enter	To view the output, type dna2. Press enter The output shows a new sequence which is a combination of string1 and string2.
Cursor on the terminal	To find the length of the new sequence, we will use len function.
Type len(dna2) press Enter	Type len within parenthesis dna2. (len(dna2)) press Enter Output shows the sequence as 15 bases long.
Type, my_seq.count("A") Press enter	We can also count the number of individual bases present in the sequence. To do so we will use count function. For example to count the number of alanines present in the sequence . Type the following command. dna2 dot count within parenthesis within doublequotes alphabet A. (dna2.count("A")) press enter The output shows the number of alanines present in the sequence dna2.
Type dna1.find(“AT”) Press enter	To find a particular base or part of the string we will use find function. Type dna2 dot find within parenthesis within doublequotes GC. dna2.find("GC") press enter The output indicates the position of the first instance of the appearance of GC in the string.
Cursor on the terminal.	Normally a sequence object cannot be edited. To edit a sequence we have to convert it to the mutable sequence object.
Type, dna3=dna2.tomutable() press enter	To do so, type, dna3 equal to dna2 dot tomutable open and close parenthesis. (dna3=dna2.tomutable()) press enter
Type dna3 press enter	For the output, type dna3 press enter
Type >>>mutable_seq[5]A Press enter	Now the sequence object can be edited. Let us replace a base from the sequence. For example to replace a base present at 5th position to alanine, type dna3 within brackets 5 equal to within double quotes alphabet A. (dna3[5]=A) Press enter For the output type dna3 press enter. Observe the output, the cytosine at position 5 is replaced with alanine.
Type, dna3[6:10]=ATGC press enter Highlight the output.	To replace a part of the string, type the following command. Dna3 within brackets 6 semicolon 10 equal to within double quotes ATGC (dna3[6:10]=ATGC) press enter For the output type dna3 press enter. The output shows the 4 bases from position the 6 to 9 are replaced with new bases ATGC.
Type, dna4=mutable_seq.toseq() For the output type, dna4 Press enter	Once you have edited your sequence object, convert it back to the “read only” form. Type the following dna4 equal to dna3 dot toseq open and close parenthesis. (dna4=dna3.toseq()) Press enter. For the output type dna4. Press enter
Slide Number 8 Summary	Let's summarize, In this tutorial, we have learnt to, 1. Generate a random DNA sequence. 2. Slice a DNA sequence at specified locations 3. Join two sequences together to form a new sequence that is to Concatenate.
Slide Number 9 Summary	4. We have also learnt how to use len, count and find functions. 5. Convert a sequence object to a mutable sequence object. 6. And replace a base or part of the string.
Slide Number 10 Assignment	For the assignment Generate a random DNA sequence of 30 bases. Using Biopython tools calculate the GC percentage and Molecular Weight of the sequence. Your completed assignment will be as follows.
GC content of the DNA sequence. Type, from Bio.SeqUtils import GC Press enter Type GC(dna) Press enter	The out put shows the GC content as percentage.
Type, from Bio.SeqUtils import molecular_weight press enter Then type, molecular_weight(dna) press enter	The output shows the molecular weight of the DNA sequence.
Slide Number 11 Acknowledgement	This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.
Slide Number 12	We Conduct workshops and give certificates. Please contact us.
Slide number 13	Spoken-Tutorial project is supported by the National Mission on Education through ICT, MHRD, Government of India
Slide number 13	This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Snehalathak