Difference between revisions of "Biopython/C2/Introduction-to-Biopython/English"
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Latest revision as of 10:46, 26 June 2015
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| Slide Number 1
Title Slide |
Welcome to this tutorial on Introduction to Biopython |
| Slide Number 2
Learning Objectives |
In this tutorial, we will learn about
|
| Slide Number 3
Pre-requisites |
To follow this tutorial you should be familiar with,
Refer to the Python tutorials at the given link. |
| Slide Number 4
System Requirement |
To record this tutorial I am using
|
| Slide Number 5.
About Biopython |
Biopython is a collection of modules for computational biology.
It can perform most basic to advanced tasks required for bioinformatics. |
| Slide number 6
Biopython functionality |
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 |
| Slide Number 7
Biopython functionality |
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. |
| Slide Number 8
Download |
Information regarding download.
Biopython package is not part of the Python distribution. It needs to be downloaded independently. For details refer the following link |
| Slide Number 9
Installation for Ubuntu/Linux systems |
Installation on Linux system.
|
| Cursor on the terminal | I have already installed Python, Ipython and Biopython on my system.
Start Ipython interpreter by typing ipython and press Enter. IPython prompt appears on screen. |
| Open the terminal and check installation of biopython | 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.
Take precaution while typing keywords, variables or functions. For instance, in the above line “i” in import is lowercase. And “B” is uppercase in Bio. |
| Cursor on the terminal. | In this tutorial, we will make use of Biopython modules to translate a DNA sequence. |
| Slide Number 10
DNA Translation |
It involves the following steps.
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| Slide Number 11
Sequence Object |
We will be using 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. |
| Open the terminal
Type: >>> from Bio.Seq import Seq |
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. |
| Cursor on the terminal. | 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. |
| >>> from Bio.Alphabet import IUPAC | 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. |
| Type >>> cdna = Seq("ATGTTACACTCCCGATGA", IUPAC.unambiguous_dna)
Press enter cdna press enter Out put Seq(ATGTTACACTCCCGATGA”, IUPAC unambiguousDNA()) |
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.
So, type: unambiguous DNA alphabet object as an argument.
The output shows the DNA sequence as a sequence object. |
| Cursor on the terminal | Let’s transcribe the coding DNA strand into the corresponding mRNA.
We will use the Seq module's built-in “transcribe” method. |
| Type
>>> mrna = coding_dna.transcribe() press enter Type mrna press enter >>> mrna Seq('AUGUUACACUCCCGAUGA', IUPACUnambiguousRNA()) |
Type the following code:
Store the output in a variable mrna.
mrna equal to cdna dot transcribe open and close parentheses press Enter.
press Enter. |
| Highlight the output | Observe the output.
|
| Cursor on the terminal | Next, to translate this mRNA to corresponding protein sequence, use the translate method. |
| Type
>>> mrna.translate() press enter Cursor on the terminal. Output: protein Seq('MLHSR*', HasStopCodon(IUPACProtein(), '*')) |
Type the following code:
protein equal to mrna dot translate open and close parentheses press Enter.
|
| Cursor on the terminal.
Output: protein Seq('MLHSR*', HasStopCodon(IUPACProtein(), '*')) |
The output shows an amino acid sequence.
The output also shows information regarding the presence of stop codons in the translated sequence.
It indicates the stop codon. |
| Cursor on the terminal. | In the above code, we have used a coding DNA strand for transcription.
In Biopython, transcribe method works only on coding DNA strand.
|
| Type ,
coding_dna = template_dna.reverse_complement() |
If you are starting with a template strand,
|
| Cursor on the terminal | Follow the rest of the code as shown above, for the coding strand. |
| Cursor on the terminal | Using methods in Biopython we have translated a DNA sequence to a protein sequence. |
| Cursor on the terminal | DNA sequence of any size can be translated to a protein using this code. |
| Slide Number 12
Summary |
Let's summarize.
In this tutorial we have learnt
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| Slide Number 13
Summary |
|
| Slide Number 14
Assignment |
Now for the assignment.
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| Cursor on the terminal. | Your completed assignment should have the following code.
Notice that, we have used 'to underscore stop' argument in the translate method.
The stop codon itself is not translated. The stop symbol is not included at the end of your protein sequence. |
| Slide Number 15
Acknowledgement |
This video summarizes the Spoken Tutorial project.
If you do not have good bandwidth, you can download and watch it. |
| Slide Number 16 | The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.
For more details, please write to us. |
| Slide number 17 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
More information on this Mission is available at this link. |
| This is Snehalatha from IIT Bombay signing off. Thank you for joining. |
