View source for Biopython/C2/Manipulating-Sequences/English-timed

{| Border=1
|'''Time'''
|'''Narration'''

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| 00:01
| Welcome to this tutorial on '''Manipulating Sequences.'''

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| 00:06
| In this tutorial, we will use '''Biopython''' tools: To generate a random DNA sequence

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| 00:13
| Slice a DNA sequence at specified locations

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| 00:17
| Join two sequences together to form a new sequence that is to concatenate 

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| 00:22
| Find the length of the sequence

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| 00:26
| Count the number of individual '''base'''s or part of the '''string'''

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| 00:31
| Find a particular base or part of the string.

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| 00:35
| Convert a '''sequence object''' to a mutable sequence object.

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| 00:40
| To follow this tutorial, you should be familiar with undergraduate Biochemistry or Bioinformatics

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| 00:47
|and basic Python programming. 

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|  00:51
|If not, refer to the '''Python''' tutorials at the given link.

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| 00:56
| To record this tutorial, I am using: * '''Ubuntu OS''' version 14.10

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| 01:03
| '''Python''' version 2.7.8

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| 01:07
| '''Ipython interpreter''' version 2.3.0

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| 01:12
|'''Biopython''' version 1.64.

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| 01:16
|Let me open the '''terminal''' and start '''ipython interpreter'''.

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| 01:21
|Press '''Ctrl, Alt''' and '''t''' keys simultaneously.

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|01:26
|At the prompt, type: "ipython" and press '''Enter'''.

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| 01:31
|'''Ipython''' prompt appears on the screen. 

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| 01:35
|Using Biopython, we can generate a '''sequence object''' for a random DNA sequence of any specified length.

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| 01:44
|Let us now generate a sequence object for a DNA sequence of 20 bases.

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|01:50
|At the prompt, type: "import random", press '''Enter'''.

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| 01:56
| Next, import '''Seq '''module from '''Bio '''package.

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| 02:01
|Often '''Seq''' is pronounced as '''seek'''.

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| 02:06
| At the prompt, type: '''From Bio dot Seq import Seq'''. Press '''Enter'''.

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| 02:15
| We will use '''Bio.Alphabet''' module to specify the alphabets in the DNA sequence.

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| 02:22
| Type: '''from Bio dot Alphabet import generic underscore dna.''' Press '''Enter'''.

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| 02:32
| Type the following '''command''' to create a sequence object for the random DNA sequence.

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| 02:38
|Store the sequence in a variable '''dna1'''.

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| 02:42
|Please note: in this command, use two single quotes instead of a double quote. Press '''Enter'''.

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| 02:50
| For the output, type: '''dna1'''. Press '''Enter'''.

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| 02:55
|  The output shows the '''sequence object''' for the random DNA sequence.

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| 03:00
| If you want a new sequence, press up-arrow key to get the same command as above. Press '''Enter'''.

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| 03:11
|For the output, type the variable name '''dna1.''' Press '''Enter'''.

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| 03:17
| The output shows a new DNA sequence which is different from the first one. 

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| 03:23
|  About '''Sequence Objects''':

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| 03:25
|The '''sequence objects''' usually act like normal '''Python string'''s.

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| 03:30
|So, follow the normal conventions as you do for Python strings.

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| 03:35
|In Python, we count the characters in the string starting from 0, instead of 1.

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| 03:41
|The first character in the sequence is position zero.

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| 03:45
| Back to the terminal. 

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| 03:47
|Often you may need to work with only a part of the sequence.

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| 03:52
|Now, let's see how to extract parts of the string and store them as sequence objects. 

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| 03:58
|For example, we will '''slice''' the DNA sequence at two positions.

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| 04:04
|First, between bases 6 and 7.

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| 04:08
|This will extract a fragment from the beginning of the sequence to the 6th base in the sequence. 

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| 04:15
|  The second slice will be between bases 11 and 12.

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| 04:20
|The second fragment will be from the 12th base to the end of the sequence. 

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| 04:26
| Type the following command, at the prompt, to extract the first fragment.

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| 04:31
|'''String1 equal to dna1 within brackets 0 colon 6.'''

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| 04:39
|'''string1''' is the variable to store the first fragment.

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| 04:43
|The rest of the command follows as in normal Python.

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| 04:47
|Enclosed in these brackets are the start and the stop positions separated by a colon. 

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| 04:53
|The positions are inclusive of the start but exclusive of the stop position. Press '''Enter'''.

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| 05:01
| To view the output, type: "string1", press '''Enter'''.

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| 05:04
|The output shows the first fragment as the sequence object.

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| 05:10
| To extract the second string from the sequence, press up-arrow key and '''edit''' the command as follows:

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| 05:17
|Change the name of the variable to '''string2''' and positions to '''11 '''and '''20'''. 

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| 05:24
| For the output, type: "string2". Press '''Enter'''.

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| 05:30
|Now we have the 2nd fragment also as a sequence object.

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| 05:34
| Let us concatenate, that is, add the two '''strings '''together to form a new fragment.

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| 05:42
|Store the new sequence in a variable '''dna2'''.

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| 05:46
|Type: '''dna2 equal to string1 plus string2'''. Press '''Enter'''.

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| 05:53
|Please note: we cannot add sequences with incompatible alphabets.

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| 05:59
|That is, we cannot concatenate a DNA sequence and a protein sequence to form a new sequence.

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| 06:07
|The two sequences must have the same alphabet attribute.

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| 06:12
| To view the output, type: "dna2". Press '''Enter'''.

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| 06:17
|The output shows a new sequence which is a combination of '''string1''' and '''string2.'''

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| 06:23
| To find the length of the new sequence, we will use '''len '''function.

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| 06:29
| Type: "len" within parenthesis "dna2". Press '''Enter'''.

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| 06:34
|Output shows the sequence as 15 bases long.

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| 06:39
| We can also count the number of individual bases present in the sequence.

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| 06:44
|To do so, we will use '''count()''' function.

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| 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.

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| 07:02
|Press '''Enter'''.

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| 07:04
|The output shows the number of alanines present in the sequence '''dna2'''. 

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| 07:10
| To find a particular base or part of the string, we will use '''find()''' function.

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| 07:16
|Type: '''dna2 dot find''' within parenthesis within double quotes "GC". Press '''Enter'''.

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| 07:26
|The output indicates the position of the first instance of the appearance of '''GC''' in the string.

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| 07:32
| Normally a sequence object cannot be edited.

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| 07:35
|To edit a sequence, we have to convert it to the mutable sequence object. 

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| 07:41
|To do so, type: '''dna3 equal to dna2 dot to mutable''' open and close parenthesis. Press '''Enter'''.

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| 07:52
| For the output, type: '''dna3'''. Press '''Enter'''. 

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| 07:55
| Now the sequence object can be edited.

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| 07:59
|Let us replace a '''base''' from the sequence. 

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| 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'''.

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| 08:19
|For the output, type: '''dna3'''. Press '''Enter'''.

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| 08:24
|Observe the output. The '''cytosine''' at position 5 is replaced with '''alanine'''. 

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| 08:31
| To replace a part of the '''string''', type the following command.

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| 08:35
|'''Dna3 within brackets 6 colon 10 equal to within double quotes ATGC.''' Press '''Enter'''.
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| 08:45
|For the output, type: '''dna3'''. Press '''Enter'''.

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| 08:52
|The output shows the 4 bases from the position  6 to 9 are replaced with new bases '''ATGC'''.

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| 09:01
| Once you have edited your sequence object, convert it back to the “read only” form.

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| 09:07
|Type the following '''dna4 equal to dna3 dot to seq open and close parenthesis'''. Press '''Enter'''.

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| 09:19
|For the output, type: '''dna4.''' Press '''Enter'''.

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| 09:25
| Let's summarize. 

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| 09:27
|In this tutorial, we have learnt to: *  Generate a random DNA sequence

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| 09:32
| Slice a DNA sequence at specified locations 

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| 09:36
| Join two sequences together to form a new sequence, that is, to concatenate. 

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| 09:43
| We have also learnt how to: * use '''len, count''' and '''find''' functions

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| 09:49
| convert a sequence object to a mutable sequence object and replace a base or part of the string.

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| 09:57
|For the assignment, generate a random '''DNA sequence''' of 30 bases. 

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| 10:02
|Using Biopython tools, calculate the GC percentage and molecular weight of the sequence. 

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| 10:09
|Your completed assignment will be as follows.

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| 10:13
|The output shows the '''GC''' content as percentage.

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| 10:18
| The output shows the molecular weight of the DNA sequence.

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| 10:23
| This video summarizes the Spoken Tutorial project.

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| 10:26
|If you do not have good bandwidth, you can download and watch it. 

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| 10:30
| We conduct workshops and give certificates.

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| 10:32
|Please contact us. 

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| 10:35
| Spoken-Tutorial project is supported by the National Mission on Education through ICT, MHRD, Government of India.

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| 10:43
| This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining. 

|}