Biopython/C2/Manipulating-Sequences/English-timed

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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.

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