Difference between revisions of "Biopython/C2/Manipulating-Sequences/English-timed"

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| In this tutorial, we will use Biopython tools:* To Generate a random DNA sequence
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| In this tutorial, we will use '''Biopython''' tools:* To generate a random DNA sequence
  
 
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|* Count the number of individual bases or part of the string
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|* Count the number of individual '''base'''s or part of the '''string'''
  
 
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|* Convert a sequence object to a mutable sequence object.
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|* Convert a '''sequence object''' to a mutable sequence object.
  
 
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|Using Biopython we can generate a sequence object for a random DNA sequence of any specified length.
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|Using Biopython, we can generate a sequence object for a random DNA sequence of any specified length.
  
 
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|01:50
 
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|At the prompt. Type'''import random''' press enter.
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|At the prompt, type: '''import random''', press '''Enter'''.
  
 
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| Next import '''Seq '''module from '''Bio '''package.
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| Next, import '''Seq '''module from '''Bio '''package.
  
 
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| At the prompt type,'''From Bio dot Seq import Seq''' . Press enter.
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| At the prompt, type: '''From Bio dot Seq import Seq'''. Press '''Enter'''.
  
 
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| Type,'''from Bio dot alphabet import generic underscore dna.''' press enter.
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| Type: '''from Bio dot alphabet import generic underscore dna.''' Press '''Enter'''.
  
 
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| 02:32
 
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| Type the following command to create a sequence object for the random DNA sequence;
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| Type the following '''command''' to create a sequence object for the random DNA sequence.
  
 
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|Store the sequence in a variable '''dna1'''
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|Store the sequence in a variable '''dna1'''.
  
 
|-
 
|-
 
| 02:42
 
| 02:42
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|Please note in this command use two single quotes instead of a double quote. Press enter.
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|Please note: in this command, use two single quotes instead of a double quote. Press '''Enter'''.
  
 
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| 02:50
 
| 02:50
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| For the output, type '''dna1'''. Press enter
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| For the output, type: '''dna1'''. Press '''Enter'''.
  
 
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| If you want a new sequence, press up arrow key to get the same command as above. Press enter.
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| 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
 
| 03:11
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|For the output, type the variable name, '''dna1.''' Press enter
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|For the output, type the variable name '''dna1.''' Press '''Enter'''.
  
 
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| 03:17
 
| 03:17
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| The output shows a new DNA sequence, which is different from the first one.  
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| The output shows a new DNA sequence which is different from the first one.  
  
 
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| 03:23
 
| 03:23
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|  About '''Sequence Objects'''
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|  About '''Sequence Objects''':
  
 
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| 03:25
 
| 03:25
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|The '''sequence objects''' usually act like normal Python strings.
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|The '''sequence objects''' usually act like normal '''Python string'''s.
  
 
|-
 
|-
 
| 03:30
 
| 03:30
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|So follow the normal conventions as you do for Python strings
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|So, follow the normal conventions as you do for Python strings.
  
 
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| 03:47
 
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|Often you many need to work with only a part of the sequence.
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|Often you may need to work with only a part of the sequence.
  
 
|-
 
|-
 
| 03:52
 
| 03:52
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|Now lets see how to extract parts of the string and store them as sequence objects.  
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|Now let's see how to extract parts of the string and store them as sequence objects.  
  
 
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| 03:58
 
| 03:58
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|For example we will slice the DNA sequence at two positions.
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|For example, we will slice the DNA sequence at two positions.
  
 
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|First between bases 6 and 7.
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|First, between bases 6 and 7.
  
 
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| Type the following command at the prompt to extract the first fragment.
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| Type the following command, at the prompt, to extract the first fragment.
  
 
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|The positions are '''inclusive''' of the start, but '''exclusive''' of the stop position. Press '''Enter'''
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|The positions are inclusive of the start but exclusive of the stop position. Press '''Enter'''.
  
 
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| 05:01
 
| 05:01
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| To view the output type, '''string1,''' Press enter.
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| To view the output, type: '''string1''', press '''Enter'''.
  
 
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| 05:10
 
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| To extract the second string from the sequence, Press up arrow key and edit the command as follows:
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| To extract the second string from the sequence, press up-arrow key and '''edit''' the command as follows:
  
 
|-
 
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| 05:17
 
| 05:17
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|Change the name of the variable to '''string2''', and positions to '''11 '''and '''20'''.  
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|Change the name of the variable to '''string2''' and positions to '''11 '''and '''20'''.  
  
 
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| 05:24
 
| 05:24
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| For the output type '''string2'''. Press enter.
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| For the output, type: '''string2'''. Press '''Enter'''.
  
 
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| Let us concatenate, that is, add the two '''strings '''together to form a new fragment:
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| Let us concatenate, that is, add the two '''strings '''together to form a new fragment.
  
 
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|Type,'''dna2 equal to string1 plus string2'''. Press enter
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|Type: '''dna2 equal to string1 plus string2'''. Press '''Enter'''.
  
 
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| 05:53
 
| 05:53
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|Please note; we cannot add sequences with incompatible alphabets.
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|Please note: we cannot add sequences with incompatible alphabets.
  
 
|-
 
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| 05:59
 
| 05:59
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|That is we cannot concatenate a DNA sequence and a protein sequence, to form a new sequence.
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|That is we cannot concatenate a DNA sequence and a protein sequence to form a new sequence.
  
 
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| To view the output, type '''dna2.''' Press enter
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| To view the output, type: '''dna2.''' Press '''Enter'''.
  
 
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| Type '''len within parenthesis dna2.''' Press enter
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| Type: '''len within parenthesis dna2.''' Press '''Enter'''.
  
 
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|To do so we will use '''count''' function.
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|To do so, we will use '''count''' function.
 
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| 06:47
 
| 06:47
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|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.'''
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|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.'''
  
 
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|Press enter
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|Press '''Enter'''.
  
 
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| To find a particular base or part of the string we will use '''find''' function.
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| To find a particular base or part of the string, we will use '''find''' function.
  
 
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| 07:16
 
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|Type '''dna2 dot find within parenthesis within doublequotes GC.''' Press enter
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|Type: '''dna2 dot find within parenthesis within double quotes GC.''' Press '''Enter'''.
  
 
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|To edit a sequence we have to convert it to the mutable sequence object.  
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|To edit a sequence, we have to convert it to the mutable sequence object.  
  
 
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| 07:41
 
| 07:41
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|To do so, type,'''dna3 equal to dna2 dot to mutable open and close parenthesis.''' Press enter
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|To do so, type: '''dna3 equal to dna2 dot to mutable open and close parenthesis.''' Press '''Enter'''.
  
 
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| For the output, type '''dna3'''. Press enter
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| For the output, type: '''dna3'''. Press '''Enter'''.
  
 
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|Let us replace a base from the sequence.  
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|Let us replace a '''base''' from the sequence.  
  
 
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|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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|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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|For the output type '''dna3'''. Press enter.
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|For the output, type: '''dna3'''. Press '''Enter'''.
  
 
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|Observe the output, the '''cytosine''' at position 5 is replaced with '''alanine'''.  
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|Observe the output. The '''cytosine''' at position 5 is replaced with '''alanine'''.  
  
 
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|'''Dna3 within brackets 6 semicolon 10 equal to within double quotes ATGC.''' Press enter
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|'''Dna3 within brackets 6 semicolon 10 equal to within double quotes ATGC.''' Press '''Enter'''.
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| 08:45
 
| 08:45
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|For the output type '''dna3'''. Press enter.
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|For the output, type: '''dna3'''. Press '''Enter'''.
  
 
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|The output shows the 4 bases from position the 6 to 9 are replaced with new bases '''''ATGC'''''.
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|The output shows the 4 bases from the position 6 to 9 are replaced with new bases '''ATGC'''.
  
 
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| Once you have edited your sequence object, convert it back to the '''“read only'''” form.
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| Once you have edited your sequence object, convert it back to the “read only” form.
  
 
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|Type the following '''dna4 equal to dna3 dot to seq open and close parenthesis'''. Press enter.
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|Type the following '''dna4 equal to dna3 dot to seq open and close parenthesis'''. Press '''Enter'''.
  
 
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| 09:19
 
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|For the output type '''dna4.''' Press enter.
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|For the output, type: '''dna4.''' Press '''Enter'''.
  
 
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| 09:27
 
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|In this tutorial, we have learnt to, Generate a random DNA sequence.
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|In this tutorial, we have learnt to: * Generate a random DNA sequence
  
 
|-
 
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| 09:32
 
| 09:32
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|Slice a DNA sequence at specified locations  
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|* Slice a DNA sequence at specified locations  
  
 
|-
 
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| 09:36
 
| 09:36
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|Join two sequences together to form a new sequence that is to Concatenate.  
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|* Join two sequences together to form a new sequence, that is, to concatenate.  
  
 
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| 09:43
 
| 09:43
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| We have also learnt how to use len, count and find functions.
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| We have also learnt how to: * use len, count and '''find''' functions
  
 
|-
 
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| 09:49
 
| 09:49
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|Convert a sequence object to a mutable sequence object and replace a base or part of the string.
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|* convert a sequence object to a mutable sequence object and replace a base or part of the string.
  
 
|-
 
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| 09:57
 
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|For the assignment Generate a random DNA sequence of 30 bases.  
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|For the assignment, generate a random DNA sequence of 30 bases.  
  
 
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|Using Biopython tools calculate the GC percentage and Molecular Weight of the sequence.  
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|Using Biopython tools, calculate the GC percentage and molecular weight of the sequence.  
  
 
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| We Conduct workshops and give certificates.
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| We conduct workshops and give certificates.
  
 
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| Spoken-Tutorial project is supported by the National Mission on Education through ICT, MHRD, Government of India
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| Spoken-Tutorial project is supported by the National Mission on Education through ICT, MHRD, Government of India.
  
 
|-
 
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| 10:43
 
| 10:43
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| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
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| This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
  
 
|}
 
|}

Revision as of 17:19, 2 August 2016

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 semicolon 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 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 doublequotes 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 semicolon 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 out put 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
10:26 If you do not have good bandwidth, you can download and watch it.
10:30 We conduct workshops and give certificates.
10:32 Please contact us.
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

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