Snehalathak at 05:16, 26 June 2015

2015-06-26T05:16:26Z

Snehalathak: Created page with " {| style="border-spacing:0;" ! Visual Cue ! Narration |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."

2015-06-01T07:25:50Z

Created page with " {| style="border-spacing:0;" ! <center>Visual Cue</center> ! <center>Narration</center> |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."

New page

{| style="border-spacing:0;"
! <center>Visual Cue</center>
! <center>Narration</center>

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''

'''Title Slide'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this tutorial on '''Introduction to Biopython'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 2'''

'''Learning Objectives'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will learn about
* Important features of '''Biopython'''.
* Information regarding download and installation on Linux Operating System.
* And '''translation''' of a DNA sequence to a protein sequence using '''Biopython''' tools.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 3'''

'''Pre-requisites'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should be familiar with,

<nowiki>* Undergraduate Biochemistry </nowiki>or Bioinformatics

<nowiki>* </nowiki>And basic''' Python''' programming

Refer to the '''Python''' tutorials at the given link.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 4'''

'''System Requirement'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial I am using

'''Ubuntu''' OS version 12.04

'''Python''' version 2.7.3

'''Ipython''' version 0.12.1

'''Biopython''' 1.58

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 5.'''

'''About Biopython'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Biopython''' is a collection of modules for computational biology.

It can perform most basic to advanced tasks required for bioinformatics.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 6'''

'''Biopython functionality '''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Biopython''' tools are used for:

1. '''Parsing''' that is extracting information from various file formats such as '''FASTA''', '''Genbank''' etc.

2. Download data from database websites such as '''NCBI''', '''ExPASY''' etc

3. Run Bioinformatic algorithms such as '''BLAST'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 7'''

'''Biopython functionality '''

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 4. It has tools for performing common operations on sequences.

For example to obtain '''complements''', '''transcription''',''' translation''' etc.

5. Code for dealing with alignments.

6. And code to split up tasks into separate processes.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 8'''

'''Download'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Information regarding download.

'''Biopython''' package is not part of the '''Python''' distribution.

It needs to be downloaded independently.

For details refer the following link

http://biopython.org/wiki/Download

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 9'''

'''Installation for Ubuntu/Linux systems'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Installation on '''linux''' system.

Install '''Python''', '''Ipython''' and '''Biopython''' packages using '''Synaptic Package Manager'''.

Prerequisite software will be installed automatically.

Additional packages must be installed for graphic outputs and plots.

Open the terminal by pressing Ctrl, Alt and T keys simultaneously.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I have already installed '''Python''', '''Ipython''' and '''Biopython''' on my system.

Start '''Ipython''' interpretor by typing '''ipython''' and press enter

'''IPython''' prompt appears on screen.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the terminal and check installation of biopython
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To check the installation of '''Biopython''',

At the prompt type:

'''import Bio''' Press enter

If you don't get any error message it means '''Biopython''' is installed.

Here let me remind you, '''Python''' language is case sensitive.

Take precaution while typing keywords, variables or functions.

For instance in the above line “i” in '''import''' is lower case.

And “B” is uppercase in '''Bio'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial we will make use of '''Biopython''' modules to translate a DNA sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 10'''

'''DNA Translation'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| It involves the following steps.

First create a '''sequence object''' for coding DNA strand.

Next '''transcription''' of coding DNA strand to mRNA.

Finally''' translation''' of mRNA to a protein sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 11'''

'''Sequence Object'''

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We will use the coding DNA strand shown on this slide as an example.

It codes for a small protein sequence.

The first step is to create a '''sequence object''' for the above coding DNA strand.

Let us go back to the terminal.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the terminal

Type:

>>> from Bio.Seq import Seq

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For creating a sequence object import the '''Seq''' module from '''Bio '''package.

The''' Seq '''module provides methods to store and process sequence objects.

At the prompt type

'''from Bio dot Seq import Seq '''

press enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Next specify the alphabets in the strand explicitly when creating your '''sequence object'''.

That is to specify whether the sequence of alphabets code for nucleotides or amino acids.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| >>> from Bio.Alphabet import IUPAC
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To do so we will use '''IUPAC '''module from '''Alphabet '''package.

At the prompt type

'''from Bio dot Alphabet import IUPAC'''

Press enter

Note that we have used import and from statements to load Seq and '''IUPAC''' modules.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type >>> cdna = Seq("ATGTTACACTCCCGATGA", IUPAC.unambiguous_dna)

Press enter

cdna

press enter

Out put

Seq(''ATGTTACACTCCCGATGA”, IUPAC unambiguousDNA())
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Store the sequence object in a variable called '''cdna'''.

At the prompt type,

'''cdna equal to Seq'''

As in normal strings enclose the sequence within double quotes and parentheses.

We know our sequence is a DNA fragment.

So type '''unambiguous DNA alphabet object''' as an argument.

For the output type,

'''cdna'''

press enter

The output shows the DNA sequence as a sequence object.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let’s transcribe the coding strand into the corresponding''' mRNA.'''

We will use the Seq module's built in '''“transcribe”''' method.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type

>>> mrna = coding_dna.transcribe()

press enter

Type

mrna press enter

>>> mrna

Seq('AUGUUACACUCCCGAUGA', IUPACUnambiguousRNA())
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Type the following code:

Store the output in a variable '''mrna'''.

At the prompt type,

'''mrna equal to cdna dot transcribe open and close parentheses'''

press enter

For the output, type''' mrna'''

press enter.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Highlight the output
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the output, the '''transcribe''' method replaces the '''Thiamin''' in the DNA sequence by '''Uracil'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Next to translate this '''mRNA''' to corresponding protein sequence, use the '''translate''' method.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type

>>> mrna.translate()

press enter

Cursor on the terminal.

Output:

protein

Seq('MLHSR*', HasStopCodon(IUPACProtein(), '*'))

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Type the following code

'''protein equal to mrna dot translate open and close parentheses'''

press enter

The translate method translates RNA or DNA sequence using the standard genetic code if unspecified.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.

Output:

protein

Seq('MLHSR*', HasStopCodon(IUPACProtein(), '*'))
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The output shows an amino acid sequence.

The output also shows information regarding the presence of '''stop codons''' in the

translated sequence.

Observe the astrix at the end of the protein sequence.

It indicates the '''stop codon'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In the above code we have used a coding DNA strand for '''transciption'''.

In '''Biopython''' '''transcribe method''' works only on coding DNA strand.

However in real biological systems the process of '''transcription''' starts with a '''template strand'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type ,

coding_dna = template_dna.reverse_complement()
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| If you are starting with a''' template strand'''<nowiki>; </nowiki>

Convert it to coding strand by using '''reverse complement method''' as shown on the terminal.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Follow the rest of the code as shown above for the coding strand.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Using methods in '''Biopython''' we have translated a DNA sequence to a protein sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| DNA sequence of any size can be translated to a protein using this code.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 12'''

'''Summary'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Lets summarize.

In this tutorial we have learnt

* Important features of '''Biopython'''.
* Information regarding download and installation on Linux OS.
* Create a sequence object for the given DNA strand.<br/>

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 13'''

'''Summary'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|
* '''Transcription''' of the DNA sequence to mRNA.
* '''Translation''' of mRNA to protein sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 14'''

Assignment
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now for the assignment,
* Translate the given DNA sequence into protein sequence.<br/> 'ATGGCCCTATAGTGTCTAAGCTAG'
* Observe the output.
* The protein sequence has an internal '''stop codon'''.
* As it happens in nature, translate the DNA till first in frame '''stop codon'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Your completed assignment should have the following code.

Notice that we have used ''''to underscore stop'''' argument in the '''translate method'''.

Notice the output,

The '''stop codon''' itself is not translated.

The stop symbol is not included at the end of your protein sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 15'''

'''Acknowledgement '''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This video summarizes the Spoken Tutorial project.

If you do not have good bandwidth, you can download and watch it.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 16'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.

For more details, please write to us.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 17'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this Mission is available at this link.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"|
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

@@ Line 39: / Line 39: @@
 *'''Python''' version 2.7.3
 *'''Ipython''' version 0.12.1
-*'''Biopython''' 1.58
+*'''Biopython''' version 1.58
 |-

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

Snehalathak at 05:16, 26 June 2015

Nancyvarkey at 11:47, 1 June 2015

Snehalathak: Created page with " {| style="border-spacing:0;" ! Visual Cue ! Narration |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."