Biopython/C2/Manipulating-Sequences/English-timed

Time	Narration
00:01	Welcome to this tutorial on Manipulating Sequences.
00:06	In this tutorial, we will use Biopython tools: To generate a random DNA sequence
00:13	Slice a DNA sequence at specified locations
00:17	Join two sequences together to form a new sequence that is to concatenate
00:22	Find the length of the sequence
00:26	Count the number of individual bases or part of the string
00:31	Find a particular base or part of the string.
00:35	Convert a sequence object to a mutable sequence object.
00:40	To follow this tutorial, you should be familiar with undergraduate Biochemistry or Bioinformatics
00:47	and basic Python programming.
00:51	If not, refer to the Python tutorials at the given link.
00:56	To record this tutorial, I am using: * Ubuntu OS version 14.10
01:03	Python version 2.7.8
01:07	Ipython interpreter version 2.3.0
01:12	Biopython version 1.64.
01:16	Let me open the terminal and start ipython interpreter.
01:21	Press Ctrl, Alt and t keys simultaneously.
01:26	At the prompt, type: "ipython" and press Enter.
01:31	Ipython prompt appears on the screen.
01:35	Using Biopython, we can generate a sequence object for a random DNA sequence of any specified length.
01:44	Let us now generate a sequence object for a DNA sequence of 20 bases.
01:50	At the prompt, type: "import random", press Enter.
01:56	Next, import Seq module from Bio package.
02:01	Often Seq is pronounced as seek.
02:06	At the prompt, type: From Bio dot Seq import Seq. Press Enter.
02:15	We will use Bio.Alphabet module to specify the alphabets in the DNA sequence.
02:22	Type: from Bio dot Alphabet import generic underscore dna. Press Enter.
02:32	Type the following command to create a sequence object for the random DNA sequence.
02:38	Store the sequence in a variable dna1.
02:42	Please note: in this command, use two single quotes instead of a double quote. Press Enter.
02:50	For the output, type: dna1. Press Enter.
02:55	The output shows the sequence object for the random DNA sequence.
03:00	If you want a new sequence, press up-arrow key to get the same command as above. Press Enter.
03:11	For the output, type the variable name dna1. Press Enter.
03:17	The output shows a new DNA sequence which is different from the first one.
03:23	About Sequence Objects:
03:25	The sequence objects usually act like normal Python strings.
03:30	So, follow the normal conventions as you do for Python strings.
03:35	In Python, we count the characters in the string starting from 0, instead of 1.
03:41	The first character in the sequence is position zero.
03:45	Back to the terminal.
03:47	Often you may need to work with only a part of the sequence.
03:52	Now, let's see how to extract parts of the string and store them as sequence objects.
03:58	For example, we will slice the DNA sequence at two positions.
04:04	First, between bases 6 and 7.
04:08	This will extract a fragment from the beginning of the sequence to the 6th base in the sequence.
04:15	The second slice will be between bases 11 and 12.
04:20	The second fragment will be from the 12th base to the end of the sequence.
04:26	Type the following command, at the prompt, to extract the first fragment.
04:31	String1 equal to dna1 within brackets 0 colon 6.
04:39	string1 is the variable to store the first fragment.
04:43	The rest of the command follows as in normal Python.
04:47	Enclosed in these brackets are the start and the stop positions separated by a colon.
04:53	The positions are inclusive of the start but exclusive of the stop position. Press Enter.
05:01	To view the output, type: "string1", press Enter.
05:04	The output shows the first fragment as the sequence object.
05:10	To extract the second string from the sequence, press up-arrow key and edit the command as follows:
05:17	Change the name of the variable to string2 and positions to 11 and 20.
05:24	For the output, type: "string2". Press Enter.
05:30	Now we have the 2nd fragment also as a sequence object.
05:34	Let us concatenate, that is, add the two strings together to form a new fragment.
05:42	Store the new sequence in a variable dna2.
05:46	Type: dna2 equal to string1 plus string2. Press Enter.
05:53	Please note: we cannot add sequences with incompatible alphabets.
05:59	That is, we cannot concatenate a DNA sequence and a protein sequence to form a new sequence.
06:07	The two sequences must have the same alphabet attribute.
06:12	To view the output, type: "dna2". Press Enter.
06:17	The output shows a new sequence which is a combination of string1 and string2.
06:23	To find the length of the new sequence, we will use len function.
06:29	Type: "len" within parenthesis "dna2". Press Enter.
06:34	Output shows the sequence as 15 bases long.
06:39	We can also count the number of individual bases present in the sequence.
06:44	To do so, we will use count() function.
06:47	For example- to count the number of alanines present in the sequence, type the following command: dna2 dot count within parenthesis within double quotes alphabet A.
07:02	Press Enter.
07:04	The output shows the number of alanines present in the sequence dna2.
07:10	To find a particular base or part of the string, we will use find() function.
07:16	Type: dna2 dot find within parenthesis within double quotes "GC". Press Enter.
07:26	The output indicates the position of the first instance of the appearance of GC in the string.
07:32	Normally a sequence object cannot be edited.
07:35	To edit a sequence, we have to convert it to the mutable sequence object.
07:41	To do so, type: dna3 equal to dna2 dot to mutable open and close parenthesis. Press Enter.
07:52	For the output, type: dna3. Press Enter.
07:55	Now the sequence object can be edited.
07:59	Let us replace a base from the sequence.
08:01	For example- to replace a base present at 5th position to alanine, type: dna3 within brackets 5 equal to within double quotes alphabet A. Press Enter.
08:19	For the output, type: dna3. Press Enter.
08:24	Observe the output. The cytosine at position 5 is replaced with alanine.
08:31	To replace a part of the string, type the following command.
08:35	Dna3 within brackets 6 colon 10 equal to within double quotes ATGC. Press Enter.
08:45	For the output, type: dna3. Press Enter.
08:52	The output shows the 4 bases from the position 6 to 9 are replaced with new bases ATGC.
09:01	Once you have edited your sequence object, convert it back to the “read only” form.
09:07	Type the following dna4 equal to dna3 dot to seq open and close parenthesis. Press Enter.
09:19	For the output, type: dna4. Press Enter.
09:25	Let's summarize.
09:27	In this tutorial, we have learnt to: * Generate a random DNA sequence
09:32	Slice a DNA sequence at specified locations
09:36	Join two sequences together to form a new sequence, that is, to concatenate.
09:43	We have also learnt how to: * use len, count and find functions
09:49	convert a sequence object to a mutable sequence object and replace a base or part of the string.
09:57	For the assignment, generate a random DNA sequence of 30 bases.
10:02	Using Biopython tools, calculate the GC percentage and molecular weight of the sequence.
10:09	Your completed assignment will be as follows.
10:13	The output shows the GC content as percentage.
10:18	The output shows the molecular weight of the DNA sequence.
10:23	This video summarizes the Spoken Tutorial project.
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10:35	Spoken-Tutorial project is supported by the National Mission on Education through ICT, MHRD, Government of India.
10:43	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Priyacst, Sandhya.np14