Biopython/C2/Manipulating-Sequences/English-timed - Revision history

Pratik kamble at 12:55, 23 March 2017

2017-03-23T12:55:31Z

Priyacst at 10:30, 10 March 2017

2017-03-10T10:30:08Z

PoojaMoolya at 07:46, 10 March 2017

2017-03-10T07:46:52Z

Sandhya.np14 at 11:55, 3 August 2016

2016-08-03T11:55:18Z

Sandhya.np14 at 11:49, 2 August 2016

2016-08-02T11:49:51Z

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Sandhya.np14 at 18:16, 1 August 2016

2016-08-01T18:16:44Z

PoojaMoolya: Created page with " {| Border=1 ! Time ! Narration |- | 00:01 | Welcome to this tutorial on '''Manipulating Sequences.''' |- | 00:06 | In this tutorial, we wi..."

2016-06-06T06:43:34Z

Created page with " {| Border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Welcome to this tutorial on '''Manipulating Sequences.''' |- | 00:06 | In this tutorial, we wi..."

New page

{| Border=1
! <center>Time</center>
! <center>Narration</center>

|-
| 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 interpretor version 2.3.0

|-
| 01:12
|Biopython version 1.64

|-
| 01:16
|Let me open the terminal and start ipython interpretor.

|-
| 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 many need to work with only a part of the sequence.

|-
| 03:52
|Now lets 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 doublequotes 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 position the 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.

|}

@@ Line 1: / Line 1: @@
 {| Border=1
-! <center>Time</center>
+|'''Time'''
-! <center>Narration</center>
+|'''Narration'''
 |-
@@ Line 10: / Line 9: @@
 |-
 | 00:06
-| In this tutorial, we will use '''Biopython''' tools: * To generate a random DNA sequence
+| In this tutorial, we will use '''Biopython''' tools: To generate a random DNA sequence
 |-

@@ Line 202: / Line 202: @@
 |-
 | 04:31
-|'''String1 equal to dna1 within brackets 0 semicolon 6.'''
+|'''String1 equal to dna1 within brackets 0 colon 6.'''
 |-
@@ Line 362: / Line 362: @@
 |-
 | 08:35
-|'''Dna3 within brackets 6 semicolon 10 equal to within double quotes ATGC.''' Press '''Enter'''.
+|'''Dna3 within brackets 6 colon 10 equal to within double quotes ATGC.''' Press '''Enter'''.
 |-
 | 08:45

@@ Line 14: / Line 14: @@
 |-
 | 00:13
-|* Slice a DNA sequence at specified locations
+| Slice a DNA sequence at specified locations
 |-
 | 00:17
-|* Join two sequences together to form a new sequence that is to concatenate
+| Join two sequences together to form a new sequence that is to concatenate
 |-
 | 00:22
-|* Find the length of the sequence
+| Find the length of the sequence
 |-
 | 00:26
-|* Count the number of individual '''base'''s or part of the '''string'''
+| Count the number of individual '''base'''s or part of the '''string'''
 |-
 | 00:31
-|* Find a particular base or part of the string.
+| Find a particular base or part of the string.
 |-
 | 00:35
-|* Convert a '''sequence object''' to a mutable sequence object.
+| Convert a '''sequence object''' to a mutable sequence object.
 |-
@@ Line 54: / Line 54: @@
 |-
 | 01:03
-|* '''Python''' version 2.7.8
+| '''Python''' version 2.7.8
 |-
 | 01:07
-|* '''Ipython interpreter''' version 2.3.0
+| '''Ipython interpreter''' version 2.3.0
 |-
 | 01:12
-|* '''Biopython''' version 1.64.
+|'''Biopython''' version 1.64.
 |-
@@ Line 295: / Line 295: @@
 | 06:44
 |To do so, we will use '''count()''' function.
 |-
 | 06:47
@@ Line 392: / Line 393: @@
 |-
 | 09:32
-|* Slice a DNA sequence at specified locations
+| Slice a DNA sequence at specified locations
 |-
 | 09:36
-|* Join two sequences together to form a new sequence, that is, to concatenate.
+| Join two sequences together to form a new sequence, that is, to concatenate.
 |-
@@ Line 404: / Line 405: @@
 |-
 | 09:49
-|* convert a sequence object to a mutable sequence object and replace a base or part of the string.
+| convert a sequence object to a mutable sequence object and replace a base or part of the string.
 |-

@@ Line 10: / Line 10: @@
 |-
 | 00:06
-| In this tutorial, we will use '''Biopython''' tools:* To generate a random DNA sequence
+| In this tutorial, we will use '''Biopython''' tools: * To generate a random DNA sequence
 |-
@@ Line 74: / Line 74: @@
 |-
 |01:26
-|At the prompt, type: '''ipython''' and press '''Enter'''.
+|At the prompt, type: "ipython" and press '''Enter'''.
 |-
@@ Line 82: / Line 82: @@
 |-
 | 01:35
-|Using Biopython, we can generate a sequence object for a random DNA sequence of any specified length.
+|Using Biopython, we can generate a '''sequence object''' for a random DNA sequence of any specified length.
 |-
@@ Line 90: / Line 90: @@
 |-
 |01:50
-|At the prompt, type: '''import random''', press '''Enter'''.
+|At the prompt, type: "import random", press '''Enter'''.
 |-
@@ Line 110: / Line 110: @@
 |-
 | 02:22
-| Type: '''from Bio dot alphabet import generic underscore dna.''' Press '''Enter'''.
+| Type: '''from Bio dot Alphabet import generic underscore dna.''' Press '''Enter'''.
 |-
@@ Line 130: / Line 130: @@
 |-
 | 02:55
-|  The output shows the sequence object for the random DNA sequence.
+|  The output shows the '''sequence object''' for the random DNA sequence.
 |-
@@ Line 158: / Line 158: @@
 |-
 | 03:35
-|In Python, we count the characters in the string starting from 0 instead of 1.
+|In Python, we count the characters in the string starting from 0, instead of 1.
 |-
@@ Line 174: / Line 174: @@
 |-
 | 03:52
-|Now let's see how to extract parts of the string and store them as sequence objects.
+|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.
+|For example, we will '''slice''' the DNA sequence at two positions.
 |-
@@ Line 214: / Line 214: @@
 |-
 | 04:47
-|Enclosed in these brackets are the start and stop positions separated by a colon.
+|Enclosed in these brackets are the start and the stop positions separated by a colon.
 |-
@@ Line 222: / Line 222: @@
 |-
 | 05:01
-| To view the output, type: '''string1''', press '''Enter'''.
+| To view the output, type: "string1", press '''Enter'''.
 |-
@@ Line 238: / Line 238: @@
 |-
 | 05:24
-| For the output, type: '''string2'''. Press '''Enter'''.
+| For the output, type: "string2". Press '''Enter'''.
 |-
@@ Line 262: / Line 262: @@
 |-
 | 05:59
-|That is we cannot concatenate a DNA sequence and a protein sequence to form a new sequence.
+|That is, we cannot concatenate a DNA sequence and a protein sequence to form a new sequence.
 |-
@@ Line 270: / Line 270: @@
 |-
 | 06:12
-| To view the output, type: '''dna2.''' Press '''Enter'''.
+| To view the output, type: "dna2". Press '''Enter'''.
 |-
@@ Line 282: / Line 282: @@
 |-
 | 06:29
-| Type: '''len within parenthesis dna2.''' Press '''Enter'''.
+| Type: "len" within parenthesis "dna2". Press '''Enter'''.
 |-
@@ Line 294: / Line 294: @@
 |-
 | 06:44
-|To do so, we will use '''count''' function.
+|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.'''
+|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.
 |-
@@ Line 309: / Line 309: @@
 |-
 | 07:10
-| To find a particular base or part of the string, we will use '''find''' function.
+| 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'''.
+|Type: '''dna2 dot find''' within parenthesis within double quotes "GC". Press '''Enter'''.
 |-
@@ Line 329: / Line 329: @@
 |-
 | 07:41
-|To do so, type: '''dna3 equal to dna2 dot to mutable open and close parenthesis.''' Press '''Enter'''.
+|To do so, type: '''dna3 equal to dna2 dot to mutable''' open and close parenthesis. Press '''Enter'''.
 |-
@@ Line 357: / Line 357: @@
 |-
 | 08:31
-| To replace a part of the string, type the following command.
+| To replace a part of the '''string''', type the following command.
 |-
@@ Line 384: / Line 384: @@
 |-
 | 09:25
-| Let's summarize,
+| Let's summarize.
 |-
 | 09:27
-|In this tutorial, we have learnt to: * Generate a random DNA sequence
+|In this tutorial, we have learnt to: *  Generate a random DNA sequence
 |-
@@ Line 400: / Line 400: @@
 |-
 | 09:43
-| We have also learnt how to: * use len, count and '''find''' functions
+| We have also learnt how to: * use '''len, count''' and '''find''' functions
 |-
@@ Line 408: / Line 408: @@
 |-
 | 09:57
-|For the assignment, generate a random DNA sequence of 30 bases.
+|For the assignment, generate a random '''DNA sequence''' of 30 bases.
 |-
@@ Line 420: / Line 420: @@
 |-
 | 10:13
-|The out put shows the GC content as percentage.
+|The output shows the '''GC''' content as percentage.
 |-
@@ Line 428: / Line 428: @@
 |-
 | 10:23
-| This video summarizes the Spoken Tutorial project
+| This video summarizes the Spoken Tutorial project.
 |-

@@ Line 10: / Line 10: @@
 |-
 | 00:06
-| In this tutorial, we will use Biopython tools To Generate a random DNA sequence .
+| In this tutorial, we will use Biopython tools:* To Generate a random DNA sequence
 |-
 | 00:13
-|Slice a DNA sequence at specified locations.
+|* Slice a DNA sequence at specified locations
 |-
 | 00:17
-| Join two sequences together to form a new sequence that is to Concatenate.
+|* Join two sequences together to form a new sequence that is to concatenate
 |-
 | 00:22
-| Find the length of the sequence.
+|* Find the length of the sequence
 |-
 | 00:26
-|Count the number of individual bases or part of the string.
+|* Count the number of individual bases or part of the string
 |-
 | 00:31
-|Find a particular base or part of the string.
+|* Find a particular base or part of the string.
 |-
 | 00:35
-|Convert a sequence object to a mutable sequence object.
+|* Convert a sequence object to a mutable sequence object.
 |-
 | 00:40
-| To follow this tutorial you should be familiar with, Undergraduate Biochemistry or Bioinformatics
+| To follow this tutorial, you should be familiar with undergraduate Biochemistry or Bioinformatics
 |-
 | 00:47
-|And Basic Python programming
+|and basic Python programming.
 |-
 |  00:51
-|If not: Refer to the Python tutorials at the given link.
+|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
+| To record this tutorial, I am using: * '''Ubuntu OS''' version 14.10
 |-
 | 01:03
-|Python version 2.7.8
+|* '''Python''' version 2.7.8
 |-
 | 01:07
-|Ipython interpretor version 2.3.0
+|* '''Ipython interpreter''' version 2.3.0
 |-
 | 01:12
-|Biopython version 1.64
+|* '''Biopython''' version 1.64.
 |-
 | 01:16
-|Let me open the terminal and start ipython interpretor.
+|Let me open the '''terminal''' and start '''ipython interpreter'''.
 |-
 | 01:21
-|Press ctrl, alt and t keys simultaneously.
+|Press '''Ctrl, Alt''' and '''t''' keys simultaneously.
 |-
 |01:26
-|At the prompt, type ipython and press enter.
+|At the prompt, type: '''ipython''' and press '''Enter'''.
 |-
 | 01:31
-|Ipython prompt appears on the screen.
+|'''Ipython''' prompt appears on the screen.
 |-