Difference between revisions of "Biopython/C2/Introduction-to-Biopython/English-timed"
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| − | |In this tutorial, we will learn about: *important features of '''Biopython''' | + | |In this tutorial, we will learn about: * important features of '''Biopython''' |
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| − | |* And | + | |* And '''translation''' of a DNA sequence to a protein sequence using '''Biopython''' tools. |
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| − | |* | + | |* and basic''' Python''' programming. |
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| − | | '''Biopython''' package is not part of the '''Python''' distribution | + | | '''Biopython''' package is not part of the '''Python''' distribution; it needs to be downloaded independently. |
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| − | | For details, refer the following link. | + | | For details, refer to the following link. |
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| − | | Start '''Ipython''' interpreter by typing | + | | Start '''Ipython''' interpreter by typing "ipython" and press '''Enter'''. |
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| − | |To check the installation of '''Biopython'''- at the prompt, type: | + | |To check the installation of '''Biopython'''- at the prompt, type: "import Bio", press '''Enter'''. |
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| − | |First, create a '''sequence object''' for coding '''DNA''' | + | |First, create a '''sequence object''' for coding '''DNA strand'''. |
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| − | |We will be using the coding | + | |We will be using the coding DNA strand shown on this slide, as an example. |
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| − | | Note that | + | | Note that we have used '''import''' and '''from''' statements to '''load''' "Seq" and "IUPAC" modules. |
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| − | | We know our sequence is a '''DNA''' fragment. So, type: '''unambiguous DNA | + | | We know our sequence is a '''DNA''' fragment. So, type: '''unambiguous DNA '''alphabet object as an '''argument'''. |
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| − | | For the output, type: '''cdna''' | + | | For the output, type: '''cdna'''. Press '''Enter'''. |
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| − | |The output shows an | + | |The output shows an amino acid sequence. |
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| − | | Observe the asterisk at the end of the | + | | Observe the asterisk at the end of the protein sequence. It indicates the '''stop codon'''. |
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| − | |In ''' | + | |In Biopython, '''transcribe''' method works only on coding DNA strand. |
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| − | |If you are starting with a''' template strand''', convert it to coding strand by using '''reverse complement | + | |If you are starting with a''' template strand''', convert it to coding strand by using '''reverse complement''' method, as shown on the terminal. |
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| − | |'''DNA''' sequence of any size can be translated to a | + | |'''DNA''' sequence of any size can be translated to a protein sequence using this code. |
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| − | |* Important features of '''Biopython''' | + | |* Important features of '''Biopython''' |
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| 07:43 | | 07:43 | ||
| − | |* Information regarding download and installation on '''Linux OS''' | + | |* Information regarding download and installation on '''Linux OS''' |
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| − | |* '''Transcription''' of the | + | |* '''Transcription''' of the DNA sequence to '''mRNA'''. |
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| − | |* '''Translation''' of '''mRNA''' to | + | |* '''Translation''' of '''mRNA''' to protein sequence. |
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| − | |Now for the assignment- | + | |Now, for the assignment- |
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| − | |The | + | |The protein sequence has an internal '''stop codon'''. |
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| − | |Notice that we have used | + | |Notice that we have used '''to underscore stop''' argument in the '''translate()''' method. Notice the output. |
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Revision as of 16:29, 3 August 2016
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| 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 to 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. |
| 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 asterisk 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. |
