Biopython/C2/Introduction-to-Biopython/English-timed - Revision history

Sandhya.np14 at 15:33, 22 December 2017

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Sandhya.np14 at 12:58, 25 July 2017

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PoojaMoolya at 07:45, 10 March 2017

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Sandhya.np14 at 10:59, 3 August 2016

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Sandhya.np14 at 12:21, 1 August 2016

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PoojaMoolya: Created page with " {| Border=1 ! Time ! Narration |- | 00:01 |Welcome to this tutorial on '''Introduction to Biopython''' |- | 00:05 |In this tutorial, we w..."

2016-06-06T06:42:51Z

Created page with " {| Border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 |Welcome to this tutorial on '''Introduction to Biopython''' |- | 00:05 |In this tutorial, we w..."

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

|-
| 00:01
|Welcome to this tutorial on '''Introduction to Biopython'''

|-
| 00:05
|In this tutorial, we will learn about important features of '''Biopython'''.

|-
| 00:10
|Information regarding download and installation on Linux Operating System.

|-
| 00:15
|And '''translation''' of a DNA sequence to a protein sequence using '''Biopython''' tools.

|-
| 00:22
|To follow this tutorial you should be familiar with,

|-
| 00:25
|Undergraduate Biochemistry or Bioinformatics

|-
| 00:29
|And basic''' Python''' programming

|-
| 00:31
|Refer to the '''Python''' tutorials at the given link.

|-
| 00:35
|To record this tutorial I am using '''Ubuntu''' OS version 12.04

|-
| 00:41
|'''Python''' version 2.7.3

|-
| 00:44
|'''Ipython''' version 0.12.1 and

|-
| 00:48
|'''Biopython''' version 1.58
|-
| 00:51
| '''Biopython''' is a collection of modules for computational biology.

|-
| 00:57
| It can perform most basic to advanced tasks required for bioinformatics.

|-
| 01:03
|'''Biopython''' tools are used for:

|-
| 01:05
| '''Parsing''' that is extracting information from various file formats such as '''FASTA''', '''Genbank''' etc.

|-
| 01:14
| Download data from database websites such as '''NCBI''', '''ExPASY''' etc

|-
| 01:22
| Run '''Bioinformatic''' algorithms such as '''BLAST'''

|-
| 01:26
|It has tools for performing common operations on sequences.

|-
| 01:31
| For example to obtain '''complements''', '''transcription''',''' translation''' etc.

|-
| 01:38
| Code for dealing with alignments.

|-
| 01:40
| And code to split up tasks into separate processes.

|-
| 01:46
|Information regarding download.

|-
| 01:48
| '''Biopython''' package is not part of the '''Python''' distribution, it needs to be downloaded independently.

|-
| 01:54
| For details refer the following link

|-
| 01:59
|Installation on '''Linux''' system.

|-
| 02:02
|Install '''Python, Ipython''' and '''Biopython''' packages using '''Synaptic Package Manager'''.

|-
| 02:08
|Prerequisite software will be installed automatically.

|-
| 02:13
| Additional packages must be installed for graphic outputs and plots.

|-
| 02:18
| Open the terminal by pressing '''Ctrl, Alt''' and '''T''' keys simultaneously.

|-
| 02:24
|I have already installed '''Python, Ipython''' and '''Biopython''' on my system.

|-
| 02:30
| Start '''Ipython''' interpreter by typing '''ipython''' and press '''Enter'''.

|-
| 02:35
| '''IPython''' prompt appears on screen.

|-
| 02:38
|To check the installation of '''Biopython''', at the prompt type: '''import Bio''' press '''Enter'''.

|-
| 02:48
| If you don't get any error message, it means '''Biopython''' is installed.

|-
| 02:54
| Here let me remind you, '''Python''' language is case sensitive.

|-
| 02:59
| Take precaution while typing keywords, variables or functions.

|-
| 03:04
| For instance, in the above line “i” in '''import''' is lowercase and “B” is uppercase in '''Bio'''.

|-
| 03:12
|In this tutorial, we will make use of '''Biopython''' modules to translate a '''DNA sequence'''.

|-
| 03:19
|It involves the following steps.

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| 03:22
|First create a '''sequence object''' for coding '''DNA''' strand.

|-
| 03:27
|Next '''transcription''' of coding '''DNA''' strand to '''mRNA'''.

|-
| 03:32
| Finally''' translation''' of '''mRNA''' to a '''protein''' sequence.

|-
| 03:37
|We will be using the coding '''DNA''' strand shown on this slide, as an example.

|-
| 03:42
| It codes for a small '''protein''' sequence.

|-
| 03:46
| The first step is to create a '''sequence object''' for the above coding '''DNA''' strand.

|-
| 03:52
|Let us go back to the '''terminal'''.

|-
| 03:55
|For creating a sequence object, import the '''Seq''' module from '''Bio '''package.

|-
| 04:02
| The''' Seq '''module provides methods to store and process sequence objects.

|-
| 04:08
| At the prompt, type '''from Bio dot Seq import Seq ''' press '''Enter'''.

|-
| 04:17
|Next, specify the alphabets in the strand explicitly, when creating your '''sequence object'''.

|-
| 04:24
| That is to specify whether the sequence of alphabets code for '''nucleotides''' or '''amino acids'''.

|-
| 04:32
|To do so we will use '''IUPAC '''module from '''Alphabet '''package.

|-
| 04:38
| At the prompt, type:'''from Bio dot Alphabet import IUPAC'''. Press '''Enter'''.

|-
| 04:48
| Note that, we have used import and from statements to load Seq and '''IUPAC''' modules.

|-
| 04:56
|Store the sequence object in a variable called '''cdna'''.

|-
| 05:01
| At the prompt, type: '''cdna equal to Seq''' as in normal strings.

|-
| 05:08
| Enclose the sequence within double quotes and parentheses.

|-
| 05:13
| We know our sequence is a '''DNA''' fragment. So, type: '''unambiguous DNA alphabet object''' as an argument.

|-
| 05:21
| For the output type: '''cdna'''; press '''Enter'''

|-
| 05:26
| The output shows the DNA sequence as a sequence object.

|-
| 05:30
|Let’s transcribe the coding '''DNA''' strand into the corresponding''' mRNA.'''

|-
| 05:35
| We will use the Seq module's built-in '''“transcribe”''' method.

|-
| 05:39
|Type the following code:

|-
| 05:41
| Store the output in a variable '''mrna'''.

|-
| 05:45
| At the prompt type,'''mrna equal to cdna dot transcribe open and close parentheses''' press '''Enter'''.

|-
| 05:55
| For the output, type''' mrna.''' Press '''Enter'''.

|-
| 06:01
|Observe the output.

|-
| 06:02
| The '''transcribe''' method replaces the '''Thiamin''' in the '''DNA''' sequence by '''Uracil'''.

|-
| 06:09
|Next, to translate this '''mRNA''' to corresponding '''protein''' sequence, use the '''translate''' method.

|-
| 06:16
|Type the following code: '''protein equal to mrna dot translate open and close parentheses'''. Press '''Enter'''.

|-
| 06:27
| The translate method translates '''RNA''' or '''DNA''' sequence using the standard genetic code, if unspecified.

|-
| 06:36
|The output shows an '''amino acid''' sequence.

|-
| 06:40
| The output also shows information regarding the presence of '''stop codons''' in the translated sequence.

|-
| 06:47
| Observe the asterix at the end of the '''protein''' sequence. It indicates the '''stop codon'''.

|-
| 06:53
|In the above code, we have used a coding '''DNA''' strand for '''transcription'''.

|-
| 06:59
|In '''Biopython, transcribe method''' works only on coding '''DNA''' strand.

|-
| 07:04
|However in real biological systems the process of '''transcription''' starts with a '''template strand'''.

|-
| 07:11
|If you are starting with a''' template strand''', convert it to coding strand by using '''reverse complement method''', as shown on the '''terminal'''.

|-
| 07:20
|Follow the rest of the code as shown above, for the coding strand.

|-
| 07:24
|Using methods in '''Biopython''' we have translated a '''DNA''' sequence to a '''protein''' sequence.

|-
| 07:31
|'''DNA''' sequence of any size can be translated to a '''protein''' sequence using this code.

|-
| 07:37
|Let's summarize.

|-
| 07:38
|In this tutorial we have learnt

|-
| 07:41
|Important features of '''Biopython'''.

|-
| 07:43
|Information regarding download and installation on '''Linux OS'''.

|-
| 07:48
|Create a sequence object for the given '''DNA''' strand.

|-
| 07:52
|'''Transcription''' of the '''DNA''' sequence to '''mRNA'''.

|-
| 07:56
|'''Translation''' of '''mRNA''' to '''protein''' sequence.

|-
| 08:00
|Now for the assignment.

|-
| 08:02
|Translate the given '''DNA''' sequence into '''protein''' sequence.

|-
| 08:06
|Observe the output.

|-
| 08:08
|The '''protein''' sequence has an internal '''stop codon'''.

|-
| 08:11
|As it happens in nature, translate the '''DNA''' till first in frame '''stop codon'''.

|-
| 08:17
|Your completed assignment should have the following code.

|-
| 08:20
|Notice that, we have used ''''to underscore stop'''' argument in the '''translate method.''' Notice the output.
|-
| 08:27
|The '''stop codon''' itself is not translated.

|-
| 08:31
|The stop symbol is not included at the end of your '''protein''' sequence.

|-
| 08:36
|This video summarizes the Spoken Tutorial project.

|-
| 08:39
|If you do not have good bandwidth, you can download and watch it.

|-
|08:43
|The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.

|-
| 08:50
|For more details, please write to us.

|-
| 08:53
|Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

|-
| 08:59
|More information on this Mission is available at this link.

|-
| 09:03
|This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

@@ Line 370: / Line 370: @@
 |-
 | 08:11
-|As it happens in nature, translate the '''DNA''' till first in frame '''stop codon'''.
+|As it happens in nature, translate the '''DNA''' till first '''in-frame stop codon'''.
 |-

@@ Line 14: / Line 14: @@
 |-
 | 00:10
-|Information regarding download and installation on Linux Operating System
+|* Information regarding download and installation on Linux Operating System
 |-
 | 00:15
-|And '''translation''' of a DNA sequence to a protein sequence using '''Biopython''' tools.
+|* And '''translation''' of a DNA sequence to a protein sequence using '''Biopython''' tools.
 |-
@@ Line 26: / Line 26: @@
 |-
 | 00:25
-| Undergraduate Biochemistry or Bioinformatics
+| undergraduate Biochemistry or Bioinformatics
 |-
@@ Line 42: / Line 42: @@
 |-
 | 00:41
-| '''Python''' version 2.7.3
+|* '''Python''' version 2.7.3
 |-
 | 00:44
-|'''Ipython''' version 0.12.1 and
+|* '''Ipython''' version 0.12.1 and
 |-
 | 00:48
-| '''Biopython''' version 1.58.
+|* '''Biopython''' version 1.58.
 |-
@@ Line 66: / Line 66: @@
 |-
 |  01:05
-|'''Parsing''', that is extracting information from various file formats such as '''FASTA''', '''Genbank''' etc.
+|* '''Parsing''', that is extracting information from various file formats such as '''FASTA''', '''Genbank''' etc.
 |-
 |  01:14
-| Download data from database websites such as '''NCBI''', '''ExPASY''' etc.
+|* Download data from database websites such as '''NCBI''', '''ExPASY''' etc.
 |-
 |  01:22
-| '''Run''' '''Bioinformatic algorithm'''s such as '''BLAST'''.
+|* '''Run''' '''Bioinformatic algorithm'''s such as '''BLAST'''.
 |-

@@ Line 10: / Line 10: @@
 |-
 | 00:05
-|In this tutorial, we will learn about: *important features of '''Biopython'''
+|In this tutorial, we will learn about: * important features of '''Biopython'''
 |-
@@ Line 18: / Line 18: @@
 |-
 | 00:15
-|* And, '''translation''' of a DNA sequence to a protein sequence using '''Biopython''' tools.
+|* And '''translation''' of a DNA sequence to a protein sequence using '''Biopython''' tools.
 |-
@@ Line 30: / Line 30: @@
 |-
 | 00:29
-|* And basic''' Python''' programming.
+|* and basic''' Python''' programming.
 |-
@@ Line 97: / Line 97: @@
 |-
 | 01:48
-| '''Biopython''' package is not part of the '''Python''' distribution, it needs to be downloaded independently.
+| '''Biopython''' package is not part of the '''Python''' distribution; it needs to be downloaded independently.
 |-
 | 01:54
-| For details, refer the following link.
+| For details, refer to the following link.
 |-
@@ Line 129: / Line 129: @@
 |-
 | 02:30
-| Start '''Ipython''' interpreter by typing '''ipython''' and press '''Enter'''.
+| Start '''Ipython''' interpreter by typing "ipython" and press '''Enter'''.
 |-
@@ Line 137: / Line 137: @@
 |-
 | 02:38
-|To check the installation of '''Biopython'''- at the prompt, type: '''import Bio'''  press '''Enter'''.
+|To check the installation of '''Biopython'''- at the prompt, type: "import Bio",  press '''Enter'''.
 |-
@@ Line 165: / Line 165: @@
 |-
 | 03:22
-|First, create a '''sequence object''' for coding '''DNA''' strand.
+|First, create a '''sequence object''' for coding '''DNA strand'''.
 |-
@@ Line 177: / Line 177: @@
 |-
 | 03:37
-|We will be using the coding '''DNA''' strand shown on this slide, as an example.
+|We will be using the coding DNA strand shown on this slide, as an example.
 |-
@@ Line 221: / Line 221: @@
 |-
 | 04:48
-| Note that, we have used '''import''' and '''from''' statements to '''load''' "Seq" and '''IUPAC''' modules.
+| Note that we have used '''import''' and '''from''' statements to '''load''' "Seq" and "IUPAC" modules.
 |-
@@ Line 237: / Line 237: @@
 |-
 |  05:13
-| We know our sequence is a '''DNA''' fragment. So, type: '''unambiguous DNA alphabet object''' as an '''argument'''.
+| We know our sequence is a '''DNA''' fragment. So, type: '''unambiguous DNA '''alphabet object as an '''argument'''.
 |-
 | 05:21
-| For the output, type: '''cdna''';  press '''Enter'''.
+| For the output, type: '''cdna'''. Press '''Enter'''.
 |-
@@ Line 293: / Line 293: @@
 |-
 | 06:36
-|The output shows an '''amino acid''' sequence.
+|The output shows an amino acid sequence.
 |-
@@ Line 301: / Line 301: @@
 |-
 | 06:47
-| Observe the asterisk at the end of the '''protein''' sequence. It indicates the '''stop codon'''.
+| Observe the asterisk at the end of the protein sequence. It indicates the '''stop codon'''.
 |-
@@ Line 309: / Line 309: @@
 |-
 | 06:59
-|In '''Biopython, transcribe method''' works only on coding '''DNA''' strand.
+|In Biopython, '''transcribe''' method works only on coding DNA strand.
 |-
@@ Line 317: / Line 317: @@
 |-
 | 07:11
-|If you are starting with a''' template strand''', convert it to coding strand by using '''reverse complement method''', as shown on the terminal.
+|If you are starting with a''' template strand''', convert it to coding strand by using '''reverse complement''' method, as shown on the terminal.
 |-
@@ Line 329: / Line 329: @@
 |-
 | 07:31
-|'''DNA''' sequence of any size can be translated to a '''protein''' sequence using this code.
+|'''DNA''' sequence of any size can be translated to a protein sequence using this code.
 |-
@@ Line 341: / Line 341: @@
 |-
 | 07:41
-|* Important features of '''Biopython'''.
+|* Important features of '''Biopython'''
 |-
 | 07:43
-|* Information regarding download and installation on '''Linux OS'''.
+|* Information regarding download and installation on '''Linux OS'''
 |-
@@ Line 353: / Line 353: @@
 |-
 | 07:52
-|* '''Transcription''' of the '''DNA''' sequence to '''mRNA'''.
+|* '''Transcription''' of the DNA sequence to '''mRNA'''.
 |-
 | 07:56
-|* '''Translation''' of '''mRNA''' to '''protein''' sequence.
+|* '''Translation''' of '''mRNA''' to protein sequence.
 |-
 | 08:00
-|Now for the assignment-
+|Now, for the assignment-
 |-
@@ Line 373: / Line 373: @@
 |-
 |  08:08
-|The '''protein''' sequence has an internal '''stop codon'''.
+|The protein sequence has an internal '''stop codon'''.
 |-
@@ Line 385: / Line 385: @@
 |-
 | 08:20
-|Notice that we have used ''''to underscore stop'''' argument in the '''translate method.''' Notice the output.
+|Notice that we have used '''to underscore stop''' argument in the '''translate()''' method. Notice the output.
 |-
 | 08:27