Biopython/C2/Introduction-to-Biopython/Khasi
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| 00:01 | Welcome to this tutorial on Introduction to Biopython.
(Ngi pdiang sngewbha ia phi sha kane ka nuksa ia ka Introduction to Biopython.)
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| 00:05 | In this tutorial, we will learn about: * important features of Biopython
(Ha kane ka nuksa , ngin ia pule shaphang ki jingmyntoi jong ka Biopython) |
| 00:10 | Information regarding download and installation on Linux Operating System
(Ki jingtip shaphang ka download bad installation jong ka Linux Operating System) |
| 00:15 | And translation of a DNA sequence to a protein sequence using Biopython tools.
(Bad ka translation jong ka DNA sekwen sha ka protein sekwen da kaba pyndonkam da ki tiar (tools) ka Biopython) |
| 00:22 | To follow this tutorial, you should be familiar with-
(Ban sngewthuh shuh shuh ia kane ka jingbatai , phi dei ban long kiba shemphang ha ka) |
| 00:25 | Undergraduate Biochemistry or Bioinformatics
(Undergraduate Biochemistry lane Bioinformatics) |
| 00:29 | and basic Python programming.
(bad ka basic Python programming) |
| 00:31 | Refer to the Python tutorials at the given link.
(Pyndonkam da ka nuksa Python ba lah ai ha ka link hapoh ) |
| 00:35 | To record this tutorial, I am using: * Ubuntu OS version 12.04
(Ban record ia kane ka nuksa , nga pyndonkam da ka * Ubuntu OS version 12.04)
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| 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 bad) |
| 00:48 | Biopython version 1.58.
(Biopython version 1.58.) |
| 00:51 | Biopython is a collection of modules for computational biology.
(Ka Biopython ka dei ka jinglum kyllum ia ki modules na ka bynta ka computational biology) |
| 00:57 | It can perform most basic to advanced tasks required for bioinformatics.
(ka lah ban trei ia kiba suk eh haduh kiba khia tam ki kam kiba donkam ha ka bioinformatics) |
| 01:03 | Biopython tools are used for:
(Ia ki tiar (tools) jong ka Biopython shait pyndonkam ha ka |
| 01:05 | Parsing, that is extracting information from various file formats such as FASTA, Genbank etc.
(Parsing, kata kaba mut ba wad jingtip na kiba bun ki file formats kum ka FASTA, Genbank, bad kumta ter ter)
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| 01:14 | Download data from database websites such as NCBI, ExPASY etc.
(Ban download data na ka database websites kum ka NCBI, ExPASY, bad kumta ter ter) |
| 01:22 | Run Bioinformatic algorithms such as BLAST.
(Ban Run ïaki Bioinformatic algorithms kum ka BLAST.) |
| 01:26 | It has tools for performing common operations on sequences.
(Ka don ia ki tiar (tools) ban trei ki kam ha ka rukom ba ryntih) |
| 01:31 | For example- to obtain complements, transcription, translation etc.
(Nuksa – ban ioh complements, transcription, translation bad kumta ter ter) |
| 01:38 | Code for dealing with alignments
(Ki code ban peit ia ka alignment) |
| 01:40 | and code to split up tasks into separate processes.
(bad ki code ban phiah ia ki kam ha ki bynta ba pher ba pher) |
| 01:46 | Information regarding download:
(Jingpyntip shaphang ban download) |
| 01:48 | Biopython package is not part of the Python distribution; it needs to be downloaded independently.
(Ka Biopython kam dei kaba wan lang bad ka Python; ngi hap ban download ïaka laka jong) |
| 01:54 | For details, refer to the following link.
(Ban tip kham bniah, peit ia ka link ba hapoh ) |
| 01:59 | Installation on Linux system:
(Ban install ha ka system Linux |
| 02:02 | Install Python, Ipython and Biopython packages using Synaptic Package Manager.
(Install ia ka Python, Ipython bad Biopythonda kaba pyndonkam da ka Synaptic Package Manager |
| 02:08 | Prerequisite software will be installed automatically.
(Ki software ba donkam kin sa install hi) |
| 02:13 | Additional packages must be installed for graphic outputs and plots.
(Ngi hap ban install hi ia ki software jong ka graphic outputs bad plots |
| 02:18 | Open the terminal by pressing Ctrl, Alt and T keys simultaneously.
(Plie ia ka terminal da kaba nion sah u Ctrl, Alt bad T key) |
| 02:24 | I have already installed Python, Ipython and Biopython on my system.
(Nga lah dep install lypa ka Python, Ipython bad Biopython ha system jong nga) |
| 02:30 | Start Ipython interpreter by typing "ipython" and press Enter.
(Plie ia ka Ipython interpreter da kaba type "ipython" bad sa nion Enter) |
| 02:35 | IPython prompt appears on screen.
(Ka IPythonprompt kan sa paw ha screen) |
| 02:38 | To check the installation of Biopython- at the prompt, type: "import Bio", press Enter.
(Ban pyntikna ba lah install ka Biopython, ha ka prompt, type "import Bio", bad sa press Enter) |
| 02:48 | If you don't get any error message, it means Biopython is installed.
(Lada phim ioh message error ei ei, ka mut ka Biopython ka lah long ) |
| 02:54 | Here, let me remind you, Python language is case sensitive.
(Hangne, ai ba ngan pynkynmaw ba ka Python language ka long case sensitive) |
| 02:59 | Take precaution while typing keywords, variables or functions.
(Da phikir bha haba type ki keywords, ki variables lane functions) |
| 03:04 | For instance, in the above line “i” in import is lowercase and “B” is uppercase in Bio.
(Kumba long, hajrong utei u lain , “i” ha import dei u lowercase bad u “B”dei u uppercase ha Bio) |
| 03:12 | In this tutorial, we will make use of Biopython modules to translate a DNA sequence.
(Ha kane ka nuksa , ngin pyndonkam da ka Biopythonmodules ban pynkylla ia ka sekwen ka DNA ) |
| 03:19 | It involves the following steps.
(Ki rukom pyndonkam ki long harum) |
| 03:22 | First, create a sequence object for coding DNA strand.
(Nyngkong eh, shna ia ka sequence object ban code ia ka DNA strand) |
| 03:27 | Next, transcription of coding DNA strand to mRNA.
(Nangta, sa ka transcription ban code ia ka DNA strand sha ka mRNA |
| 03:32 | Finally, translation of mRNA to a protein sequence.
(Khatduh eh, translation jong ka mRNA sha ka protein sekwen ) |
| 03:37 | We will be using the coding DNA strand shown on this slide, as an example.
(Ngin pyndonkam ia ka coding DNA strand kumba lah pyni ha ka slide, kum ka nuksa) |
| 03:42 | It codes for a small protein sequence.
(Ka pyndonkam code da u protein sekwen barit |
| 03:46 | The first step is to create a sequence object for the above coding DNA strand.
(Nyngkong eh ngi dei ban shna ia ka sekwen object na ka bynta ka coding DNA strand kaba hajrong) |
| 03:52 | Let us go back to the terminal.
(To ngin ia phai biang sha ka terminal) |
| 03:55 | For creating a sequence object, import the Seq module from Bio package.
(Ban shna ia ka sekwen object, wanrah ka Seq module na ka Bio package) |
| 04:02 | The Seq module provides methods to store and process sequence objects.
( Ka Seq module ka ai jingmyntoi ban pyllang bad ban shna ia ki sekwen objects) |
| 04:08 | At the prompt, type: from Bio dot Seq import Seq press Enter.
(Ha ka prompt, type: from Bio dot Seq import Seq bad sa nion Enter |
| 04:17 | Next, specify the alphabets in the strand explicitly, when creating your sequence object.
(Nangta, pyntikna ia ki alphabets ha ka strand lakajong , haba shna ia ka sequence object j |
| 04:24 | That is to specify whether the sequence of alphabets code for nucleotides or amino acids.
(Kata ka mut ban pynthikna ia ka sekwen jong ki alphabets code na ka bynta ka nucleotides lane amino acids) |
| 04:32 | To do so, we will use IUPAC module from Alphabet package.
(Ban leh ia kane , ngin pyndonkam da ka IUPAC module na ka Alphabet package) |
| 04:38 | At the prompt, type: from Bio dot Alphabet import IUPAC. Press Enter.
(Ha ka prompt, type: from Bio dot Alphabet import IUPAC. Sa nion Enter) |
| 04:48 | Note that we have used import and from statements to load "Seq" and "IUPAC" modules.
(Kynmaw ba ngi lah pyndonkam import bad from kyntien (statements) ban load "Seq" bad "IUPAC" modules) |
| 04:56 | Store the sequence object in a variable called cdna.
(Lum ia ki sekwen object ha ka variable kaba kyrteng cdna |
| 05:01 | At the prompt, type: cdna equal to Seq as in normal strings.
(Ha ka prompt, type: cdna equal to Seq kum kaba normal string |
| 05:08 | Enclose the sequence within double quotes and parentheses.
(Pyndait lang ka sekwen hapoh ki double quotes bad parentheses) |
| 05:13 | We know our sequence is a DNA fragment. So, type: unambiguous DNA alphabet object as an argument.
(Ngi tip ba ka sekwen jong ngi ka dei ka DNA ba lyngkhot (fragment). Te, type unambiguous DNA alphabet object kum ka argument) |
| 05:21 | For the output, type: cdna. Press Enter.
(Na ka bynta ka output, type: cdna. Nion Enter)
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| 05:26 | The output shows the DNA sequence as a sequence object.
(Ka output ka pyni ia ka DNA sequence kum ka sekwen object) |
| 05:30 | Let’s transcribe the coding DNA strand into the corresponding mRNA.
(To ngin ia thoh shai (transcribe) ia ka coding DNA strand sha ka corresponding mRNA.) |
| 05:35 | We will use the Seq module's built-in “transcribe” method.
(Ngin pyndonkam da ka rukom Seq module's built-in “transcribe”) |
| 05:39 | Type the following code:
(Thoh ia ki code kiba harum) |
| 05:41 | Store the output in a variable mrna.
(Lum ia ka output ha ka variable mrna) |
| 05:45 | At the prompt, type: mrna equal to cdna dot transcribe open and close parentheses, press Enter.
(Ha ka prompt, thoh : mrna equal to cdna dot transcribe open and close parentheses, nion Enter) |
| 05:55 | For the output, type: mrna. Press Enter.
(Na ka bynta ka output, thoh : mrna. Nion Enter) |
| 06:01 | Observe the output.The transcribe method replaces the Thiamin in the DNA sequence by Uracil.
(Peit ia ka output. Ka rukom transcribe kan bujli ia ka Thiamin ha ka DNA sekwen da ka Uracil) |
| 06:09 | Next, to translate this mRNA to corresponding protein sequence, use the translate method.
(Hadien , ban translate ia kane ka mRNA sha ka corresponding protein sekwen , pyndonkam da ka rukom jong ka translate) |
| 06:16 | Type the following code: protein equal to mrna dot translate open and close parentheses. Press Enter.
(Thoh ia kine ki code : protein equal to mrna dot translate open and close parentheses. Nion Enter) |
| 06:27 | The translate method translates RNA or DNA sequence using the standard genetic code, if unspecified.
(Ka rukom translate kan translate RNA lane DNA sekwen da kaba pyndom ia ka standard genetic code) |
| 06:36 | The output shows an amino acid sequence.
(Ka output kan pyni ia ka amino acid sekwen ) |
| 06:40 | The output also shows information regarding the presence of stop codons in the translated sequence.
(Ka output kan pyni ruh ia ka jingpyntip ia ka jingdon jong ka stop codons ha ka sekwen ba lah pykylla (translate) |
| 06:47 | Observe the asterisk at the end of the protein sequence. It indicates the stop codon.
(Peit ia u asterisk ha kaba kut jong ka protein sekwen . Ka pyni ia ka stop codon.) |
| 06:53 | In the above code, we have used a coding DNA strand for transcription.
(Ha u code ba ha jrong, ngi lah pyndonkam ia u coding DNA strand na ka bynta ka transcription) |
| 06:59 | In Biopython, transcribe method works only on coding DNA strand.
(Ha Biopython, ka transcribemethod ka treikam tang ha ka coding DNA strand) |
| 07:04 | However, in real biological systems, the process of transcription starts with a template strand.
(Hynrei, ha ka biological system ba shisha, ka rukom long jong ka transcription ka sdang da ka 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.
(Lada phi sdang da ka template strand, pynkylla ia ka sha ka coding strand da kaba pyndonkam da ka reverse complement method, kumba lah pyni ha ka terminal.) |
| 07:20 | Follow the rest of the code as shown above, for the coding strand.
(Leh ia kiba sah ki code kumba lah pyni hajrong, na ka bynta ka coding strand) |
| 07:24 | Using methods in Biopython we have translated a DNA sequence to a protein sequence.
(Da kaba pyndonkam da ki rukom ha Biopython ngi la dep ban pynkylla (translated) ia ka DNA sekwen sha ka protein sekwen ) |
| 07:31 | DNA sequence of any size can be translated to a protein sequence using this code.
(Ka DNA sekwen kaba ha kano kano ka size lah ban pynkylla sha ka protein sekwen da kaba pyndonkam da une u code) |
| 07:37 | Let's summarize.In this tutorial, we have learnt:
(To ngin ia pynkut . Ha kane ka nuksa , ngi leh shaphang:) |
| 07:41 | Important features of Biopython
(Ki mat ba donkam ka Biopython) |
| 07:43 | Information regarding download and installation on Linux OS
(Jingpyntip shaphang ka download bad installation ha Linux OS) |
| 07:48 | Create a sequence object for the given DNA strand.
(Ban shna sekwen object na ka bynta ka DNA strand) |
| 07:52 | Transcription of the DNA sequence to mRNA.
(Transcription jong ka DNA sekwen sha ka mRNA) |
| 07:56 | Translation of mRNA to protein sequence.
(Translation jong ka mRNA sha ka protein sekwen ) |
| 08:00 | Now, for the assignment-
(Mynta, na ka bynta ki kam ) |
| 08:02 | Translate the given DNA sequence into protein sequence.
(Pynkylla ka DNA sekwen ba lah ai sha ka protein sekwen ) |
| 08:06 | Observe the output.
(Peit ia ka output) |
| 08:08 | The protein sequence has an internal stop codon.
(Ka protein sekwen ka don lypa ka stop codon) |
| 08:11 | As it happens in nature, translate the DNA till first in frame stop codon.
(Kumba ka ju long shisha, pynkylla ia ka DNA shaduh kaba nyngkong ka frame stop codon) |
| 08:17 | Your completed assignment should have the following code.
(Ka kam ba lah dep jong phi ka dei ban don ki code kiba harum) |
| 08:20 | Notice that we have used to underscore stop argument in the translate() method. Notice the output.
(To khmih bha ba ngi lah pyndonkam ka rukom (argument)to underscore stop ha ka translate() method. Peit ka output) |
| 08:27 | The stop codon itself is not translated.
(U stop codon marwei khlem shah pynkylla) |
| 08:31 | The stop symbol is not included at the end of your protein sequence.
(U symbol sangeh u khlem shah kynthup ha kaba kut ka protein sekwen ) |
| 08:36 | This video summarizes the Spoken Tutorial project.
(Kane ka video ka lum kyllum ia ka Spoken Tutorial project) |
| 08:39 | If you do not have good bandwidth, you can download and watch it.
(Lada phim don ka bandwidth ba bha, phi lah ban download bad peit ia ka) |
| 08:43 | The Spoken Tutorial Project team conducts workshops and gives certificates for those who pass an online test.
(Ka Spoken Tutorial Project team ka shait pynlong workshop bad ai ruh ia ki khusnam certificates na ka bynta kito ba pass ia ka online test) |
| 08:50 | For more details, please write to us.
(Ban tip kham bniah, sngewbha thoh sha ngi) |
| 08:53 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
(Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Government of India) |
| 08:59 | More information on this mission is available at this link.
(Na ka bynta ki jingtip ba kham pura jong kane ka mission phin lap ha kane ka link) |
| 09:03 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining.
(Ha kaba kut, Nga dei ka Snehalatha na IIT Bombay. Khublei shibun |
