Difference between revisions of "Biopython/C2/Introduction-to-Biopython/Khasi"

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{| Border=1
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{| border=1
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! <center>Time</center>
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| '''Time'''
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! <center>Narration</center>
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| '''Narration'''
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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'''.)
+
  
 +
|-
 +
|00:01
 +
| Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka '''Introduction to Biopython'''.
  
 
|-
 
|-
−
| 00:05
+
|00:05  
−
|In this tutorial, we will learn about: * important features of '''Biopython'''
+
|Ha kane ka tutorial, ngin ia pule shaphang ki jingling ba kongsan jong ka '''Biopython'''
−
(Ha kane ka nuksa , ngin ia pule shaphang ki jingmyntoi  jong ka '''Biopython''')
+
  
 
|-
 
|-
−
| 00:10
+
|00:10
−
|Information regarding download and installation on Linux Operating System
+
|Ki jingpyntip shaphang ban download bad ban install ha ka Linux Operating System
−
(Ki jingtip  shaphang ka  download bad installation  jong  ka Linux Operating System)
+
  
 
|-
 
|-
 
| 00:15
 
| 00:15
−
|And '''translation''' of a DNA sequence to a protein sequence using '''Biopython''' tools.
+
| Bad ka '''translation''' ia ka DNA sequence sha ka protein sequence pyndonkam da ki tiar ka '''Biopython'''
−
(Bad ka '''translation''' jong  ka DNA sekwen  sha ka protein sekwen da kaba pyndonkam da ki tiar (tools)  ka '''Biopython''')
+
  
 
|-
 
|-
 
| 00:22
 
| 00:22
−
|To follow this tutorial, you should be familiar with-
+
| Ban bud ia kane ka tutorial, phi dei ban tip bha ia ka
−
(Ban sngewthuh shuh shuh  ia kane ka jingbatai , phi dei ban long kiba shemphang ha  ka)
+
  
 
|-
 
|-
−
| 00:25
+
|00:25
−
| Undergraduate Biochemistry or Bioinformatics
+
| Undergraduate Biochemistry lane Bioinformatics
−
(Undergraduate Biochemistry lane Bioinformatics)
+
  
 
|-
 
|-
−
| 00:29
+
|00:29
−
| and basic''' Python''' programming.
+
| bad ka basic ''' Python''' programming
−
(bad ka basic ''' Python''' programming)
+
  
 
|-
 
|-
−
| 00:31
+
|00:31
−
|Refer to the '''Python''' tutorials at the given link.
+
| Peit ia ki ''Python''' tutorial ha ka link bala ai
−
(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)
+
  
 +
|-
 +
|00:35
 +
| Ban record ia kane ka tutorial, nga pyndonkam da ka * '''Ubuntu OS''' version 12.04
  
 
|-
 
|-
−
| 00:41
+
| 00:41  
−
| '''Python''' version 2.7.3
+
|'''Python''' version 2.7.3
−
('''Python''' version 2.7.3)
+
  
 
|-
 
|-
 
| 00:44
 
| 00:44
−
|'''Ipython''' version 0.12.1 and
+
| '''Ipython''' version 0.12.1 bad
−
('''Ipython''' version 0.12.1 bad)
+
  
 
|-
 
|-
 
| 00:48
 
| 00:48
 
| '''Biopython''' version 1.58.
 
| '''Biopython''' version 1.58.
−
('''Biopython''' version 1.58.)
 
  
 
|-
 
|-
−
| 00:51
+
|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
−
(Ka '''Biopython''' ka dei ka jinglum kyllum ia ki modules na ka bynta ka computational biology)
+
  
 
|-
 
|-
−
| 00:57
+
|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
−
(ka lah ban trei ia kiba suk eh haduh kiba khia tam ki kam kiba donkam ha ka bioinformatics)
+
  
 
|-
 
|-
−
| 01:03
+
|01:03
−
|'''Biopython''' tools are used for:
+
| Ia ki tiar jong ka '''Biopython''' lah ju pyndonkam na ka bynta
−
(Ia ki tiar (tools)  jong ka '''Biopython''' shait  pyndonkam ha ka
+
  
 
|-
 
|-
−
| 01:05
+
|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
−
('''Parsing''', kata kaba mut ba wad jingtip na kiba bun ki file formats kum ka '''FASTA''', '''Genbank''', bad kumta ter ter)
+
−
 
+
  
 
|-
 
|-
−
| 01:14
+
|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
−
(Ban download data na ka database websites kum ka '''NCBI''', '''ExPASY''', bad kumta ter ter)
+
  
 
|-
 
|-
−
| 01:22
+
|01:22
−
| '''Run''' '''Bioinformatic algorithm'''s such as '''BLAST'''.
+
|Ban '''Run''' ïaki '''Bioinformatic algorithm'''s kum ka '''BLAST'''.
−
(Ban '''Run''' ïaki '''Bioinformatic algorithm'''s kum ka '''BLAST'''.)
+
  
 
|-
 
|-
−
| 01:26
+
|01:26
−
|It has tools for performing common operations on sequences.
+
| Ka don ia ki tools ban trei ki kam ha ka rukom ba ryntih
−
(Ka don ia ki tiar  (tools) ban trei ki kam ha ka rukom ba ryntih)
+
  
 
|-
 
|-
−
| 01:31
+
| 01:31  
−
| For example- to obtain '''complements''', '''transcription''',''' translation''' etc.
+
|Kum ka nuksa – ban ioh '''complements''', '''transcription''',''' translation''' bad kumta ter ter  
−
(Nuksa  – ban ioh '''complements''', '''transcription''',''' translation''' bad kumta ter ter)
+
  
 
|-
 
|-
 
| 01:38
 
| 01:38
−
| Code for dealing with alignments
+
|Ki code ban peit ia ka alignment
−
(Ki code ban peit ia ka alignment)
+
  
 
|-
 
|-
 
|  01:40
 
|  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
−
(bad ki code ban phiah ia ki kam ha ki bynta ba pher ba pher)
+
  
 
|-
 
|-
 
| 01:46
 
| 01:46
−
|Information regarding download:
+
| Jingpyntip shaphang ban download
−
(Jingpyntip shaphang ban download)
+
  
 
|-
 
|-
−
| 01:48
+
| 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  
−
(Ka '''Biopython''' kam dei kaba wan lang bad ka '''Python'''; ngi hap ban download ïaka laka jong)
+
  
 
|-
 
|-
 
| 01:54
 
| 01:54
−
| For details, refer to the following link.
+
| Ban tip kham bniah, peit ia ka link ba harum.
−
(Ban tip kham bniah, peit ia ka link ba hapoh )
+
  
 
|-
 
|-
 
| 01:59
 
| 01:59
−
|Installation on '''Linux''' system:
+
| Ban install ha ka system '''Linux'''
−
(Ban install ha ka system '''Linux'''
+
  
 
|-
 
|-
 
| 02:02
 
| 02:02
−
|Install '''Python, Ipython''' and '''Biopython''' packages using '''Synaptic Package Manager'''.
+
| Install ia ka '''Python, Ipython''' bad '''Biopython'''da kaba pyndonkam da ka '''Synaptic Package Manager'''
−
(Install ia ka '''Python, Ipython''' bad '''Biopython'''da kaba pyndonkam da ka '''Synaptic Package Manager'''
+
  
 
|-
 
|-
 
| 02:08
 
| 02:08
−
|Prerequisite software will be installed automatically.
+
| Ki software ba donkam kin sa install hi
−
(Ki software ba donkam kin sa install hi)
+
  
 
|-
 
|-
−
| 02:13
+
| 02:13  
−
| Additional packages must be installed for '''graphic output'''s and '''plot'''s.
+
| Ngi hap ban install hi ia ki software jong ka '''graphic output'''s bad '''plot'''s
−
(Ngi hap ban install hi ia ki software jong ka '''graphic output'''s bad '''plot'''s
+
  
 
|-
 
|-
 
| 02:18
 
| 02:18
−
| Open the '''terminal''' by pressing '''Ctrl, Alt''' and '''T''' keys simultaneously.
+
| Plie ia ka '''terminal''' da kaba nion lang ia u '''Ctrl, Alt''' bad '''T''' key
−
(Plie ia ka '''terminal''' da kaba nion sah  u '''Ctrl, Alt''' bad '''T''' key)
+
  
 
|-
 
|-
 
| 02:24
 
| 02:24
−
|I have already installed '''Python, Ipython''' and '''Biopython''' on my system.
+
| Nga lah dep install lypa ia ka '''Python, Ipython''' bad '''Biopython''' ha system jong nga
−
(Nga lah dep install lypa ka '''Python, Ipython''' bad '''Biopython''' ha system jong nga)
+
  
 
|-
 
|-
 
| 02:30
 
| 02:30
−
| Start '''Ipython''' interpreter by typing "ipython" and press '''Enter'''.
+
| Plie ia ka '''Ipython''' interpreter da kaba type "ipython" bad sa nion '''Enter'''
−
(Plie ia ka '''Ipython''' interpreter da kaba type "ipython" bad sa nion '''Enter''')
+
  
 
|-
 
|-
−
| 02:35  
+
| 02:35
−
| '''IPython''' prompt appears on screen.
+
|Ka '''IPython'''prompt ka paw ha screen
−
(Ka '''IPython'''prompt kan sa  paw ha screen)
+
  
 
|-
 
|-
−
| 02:38
+
| 02:38
−
|To check the installation of '''Biopython'''- at the prompt, type: "import Bio",  press '''Enter'''.
+
|Ban pyntikna ba lah install ia ka'''Biopython''', ha ka prompt, type "import Bio",  bad sa press '''Enter'''
−
(Ban pyntikna ba lah install ka '''Biopython''', ha ka prompt, type "import Bio",  bad sa press '''Enter''')
+
  
 
|-
 
|-
−
| 02:48
+
| 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''' lah install
−
(Lada phim ioh message error ei ei, ka mut ka '''Biopython''' ka lah long )
+
  
 
|-
 
|-
−
| 02:54
+
| 02:54  
−
| Here, let me remind you, '''Python''' language is case sensitive.
+
| Hangne, to ngan pynkynmaw ia phi ba ka'''Python''' language ka long case sensitive
−
(Hangne, ai ba  ngan pynkynmaw ba ka '''Python''' language ka long case sensitive)
+
  
 
|-
 
|-
−
| 02:59
+
| 02:59  
−
| Take precaution while typing keywords, variables or '''function'''s.
+
| Da phikir bha haba type ki keywords, ki variables lane '''function'''s
−
(Da phikir bha haba type ki keywords, ki variables lane '''function'''s)
+
  
 
|-
 
|-
−
| 03:04
+
| 03:04  
−
| For instance, in the above line “i” in '''import''' is lowercase and “B” is uppercase in '''Bio'''.
+
| Kumba long, u lain haneng, u, “i” ha '''import''' dei u lowercase bad u “B”dei u uppercase ha '''Bio'''
−
(Kumba long, hajrong utei u lain , “i” ha '''import''' dei u lowercase bad u “B”dei u uppercase ha '''Bio''')
+
  
 
|-
 
|-
−
| 03:12
+
| 03:12  
−
|In this tutorial, we will make use of '''Biopython''' modules to translate a '''DNA sequence'''.
+
| Ha kane ka tutorial, ngin pyndonkam da ka '''Biopython'''modules ban pynkylla ia ka '''DNA sequence'''  
−
(Ha kane ka nuksa , ngin pyndonkam da ka '''Biopython'''modules ban pynkylla ia ka sekwen ka '''DNA''' )
+
  
 
|-
 
|-
−
| 03:19
+
| 03:19  
−
|It involves the following steps.
+
| Ki rukom pyndonkam ki long harum
−
(Ki rukom pyndonkam ki long harum)
+
  
 
|-
 
|-
−
| 03:22
+
| 03:22  
−
|First, create a '''sequence object''' for coding '''DNA strand'''.
+
| Nyngkong eh, shna ia ka '''sequence object''' ban code ia ka '''DNA strand'''
−
(Nyngkong eh, shna ia ka '''sequence object''' ban code ia ka '''DNA strand''')
+
  
 
|-
 
|-
−
| 03:27
+
| 03:27  
−
|Next, '''transcription''' of coding '''DNA''' strand to '''mRNA'''.
+
|Nangta, sa ka '''transcription''' ban code ia ka '''DNA''' strand sha ka '''mRNA'''
−
(Nangta, sa ka '''transcription''' ban code ia ka '''DNA''' strand sha ka '''mRNA'''
+
  
 
|-
 
|-
−
| 03:32
+
| 03:32  
−
| Finally,''' translation''' of '''mRNA''' to a '''protein''' sequence.
+
| Khatduh eh, ''' translation''' jong ka '''mRNA''' sha ka '''protein''' sequence.
−
(Khatduh eh, ''' translation''' jong ka '''mRNA''' sha ka '''protein''' sekwen )
+
  
 
|-
 
|-
−
| 03:37
+
| 03:37
−
|We will be using the coding DNA strand shown on this slide, as an example.
+
|Ngin pyndonkam da ka coding DNA strand kumba lah pyni ha ka slide, kum ka nuksa
−
(Ngin pyndonkam ia  ka coding DNA strand kumba lah pyni ha ka slide, kum ka nuksa)
+
  
 
|-
 
|-
−
| 03:42
+
| 03:42  
−
| It codes for a small '''protein''' sequence.
+
| Ka code naka bynta u '''protein''' sequence barit
−
(Ka pyndonkam code da u '''protein''' sekwen  barit
+
  
 
|-
 
|-
−
| 03:46
+
| 03:46  
−
| The first step is to create a '''sequence object'''  for the above coding '''DNA''' strand.
+
| ka synjam ba nyngkong ka dei ban shna ia ka '''sequence object''' na ka bynta ka coding '''DNA''' strand kaba hajrong
−
(Nyngkong eh ngi  dei ban shna ia ka '''sekwen object''' na ka bynta ka coding '''DNA''' strand kaba hajrong)
+
  
 
|-
 
|-
−
| 03:52
+
| 03:52
−
|Let us go back to the '''terminal'''.
+
|To ngin ia phai biang sha ka '''terminal'''
−
(To ngin ia phai biang sha ka '''terminal''')
+
  
 
|-
 
|-
−
| 03:55
+
| 03:55  
−
|For creating a sequence object, import the '''Seq''' module from '''Bio '''package.
+
|Ban shna ia ka sequence object, import ïaka ka '''Seq''' module na ka '''Bio ''' package
−
(Ban shna ia ka sekwen  object, wanrah  ka '''Seq''' module na ka '''Bio ''' package)
+
  
 
|-
 
|-
−
| 04:02
+
| 04:02
−
| The''' Seq '''module provides methods to store and process sequence objects.
+
| Ka ''' Seq '''module ka ai iaki rukom ban pyllang bad ban shna ia ki sequence objects
−
( Ka ''' Seq '''module ka ai jingmyntoi  ban pyllang bad ban shna ia ki sekwen  objects)
+
  
 
|-
 
|-
−
| 04:08
+
| 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'''
−
(Ha ka prompt, type: '''from Bio dot Seq import Seq ''' bad sa nion '''Enter'''
+
  
 
|-
 
|-
 
|  04:17
 
|  04:17
−
|Next, specify the alphabets in the strand explicitly, when creating your '''sequence object'''.
+
| Nangta, batai shai ia ki alphabets ha ka strand, haba shna ia ka '''sequence object''' jong phi.
−
(Nangta, pyntikna  ia ki alphabets ha ka strand lakajong , haba shna ia ka '''sequence object''' j
+
  
 
|-
 
|-
−
|  04:24
+
|  04:24  
−
| That is to specify whether the sequence of alphabets code for '''nucleotides''' or '''amino acids'''.
+
|Kata ban thikna lada ia ka sequence jong ki alphabets code na ka bynta ka '''nucleotides''' lane '''amino acids'''
−
(Kata ka mut ban pynthikna  ia ka sekwen  jong ki alphabets code na ka bynta ka '''nucleotides''' lane '''amino acids''')
+
  
 
|-
 
|-
−
| 04:32
+
| 04:32  
−
|To do so, we will use '''IUPAC '''module from '''Alphabet '''package.
+
| Ban leh kumta, ngin pyndonkam da ka '''IUPAC '''module na ka '''Alphabet '''package
−
(Ban leh ia kane , ngin pyndonkam da ka '''IUPAC '''module na ka '''Alphabet '''package)
+
  
 
|-
 
|-
−
| 04:38
+
| 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'''
−
(Ha ka prompt, type: '''from Bio dot Alphabet import IUPAC'''. Sa nion '''Enter''')
+
  
 
|-
 
|-
−
| 04:48
+
| 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''' statements ban '''load''' "Seq" bad "IUPAC" modules
−
(Kynmaw ba ngi lah pyndonkam '''import''' bad '''from''' kyntien  (statements) ban '''load''' "Seq" bad "IUPAC" modules)
+
  
 
|-
 
|-
−
| 04:56
+
| 04:56
−
|Store the sequence object in a variable called '''cdna'''.
+
|Buh ia u sequence object ha ka variable kaba kyrteng '''cdna'''
−
(Lum ia ki sekwen  object ha ka variable kaba kyrteng '''cdna'''
+
  
 
|-
 
|-
−
| 05:01
+
| 05:01  
−
| At the prompt, type: '''cdna equal to Seq''' as in normal '''string'''s.
+
|Ha ka prompt, type: '''cdna equal to Seq''' kum ha ki normal '''string'''
−
(Ha ka prompt, type: '''cdna equal to Seq''' kum kaba  normal '''string'''
+
  
 
|-
 
|-
−
| 05:08
+
| 05:08  
−
| Enclose the sequence within double quotes and parentheses.
+
| Pyndait ia ki sequence hapoh ki double quotes bad parentheses
−
(Pyndait lang ka sekwen  hapoh ki double quotes bad parentheses)
+
  
 
|-
 
|-
 
|  05:13
 
|  05:13
−
| We know our sequence is a '''DNA''' fragment. So, type: '''unambiguous DNA '''alphabet object as an '''argument'''.
+
| Ngi tip ba ka sequence jong ngi ka dei ka '''DNA''' ba lyngkhot. Te, type '''unambiguous DNA '''alphabet object kum ka '''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
 
| 05:21
−
| For the output, type: '''cdna'''. Press '''Enter'''.
+
| Na ka bynta ka output, type: '''cdna'''. Nion '''Enter'''
−
(Na ka bynta ka output, type: '''cdna'''. Nion '''Enter''')
+
−
 
+
−
 
+
−
 
+
  
 
|-
 
|-
−
| 05:26
+
| 05:26
−
| The output shows the '''DNA sequence''' as a sequence object.
+
|Ka output ka pyni ia ka '''DNA sequence''' kum ka sequence object
−
(Ka output ka pyni ia ka '''DNA sequence''' kum ka sekwen  object)
+
  
 
|-
 
|-
−
| 05:30
+
| 05:30  
−
|Let’s transcribe the coding '''DNA''' strand into the corresponding''' mRNA.'''
+
| To ngin thoh ia ka coding '''DNA''' strand sha ka ''' mRNA.''' Ba ïadei bad kane.
−
(To ngin ia thoh shai (transcribe)  ia ka coding '''DNA''' strand sha ka corresponding  ''' mRNA.''')
+
  
 
|-
 
|-
−
| 05:35  
+
| 05:35
−
| We will use the '''Seq''' module's built-in '''“transcribe”''' method.
+
| Ngin pyndonkam da ka rukom  '''Seq''' module's built-in “transcribe”'''
−
(Ngin pyndonkam da ka rukom  '''Seq''' module's built-in “transcribe”''')
+
  
 
|-
 
|-
−
| 05:39
+
| 05:39  
−
|Type the following code:
+
| Type ia ki code kiba harum  
−
(Thoh  ia ki code kiba harum)
+
  
 
|-
 
|-
−
| 05:41
+
| 05:41  
−
| Store the output in a variable '''mrna'''.
+
|Buh ia ka output ha ka variable '''mrna'''
−
(Lum  ia ka output ha ka variable '''mrna''')
+
  
 
|-
 
|-
−
|  05:45
+
|  05:45  
−
| At the prompt, type: '''mrna equal to cdna dot transcribe open and close parentheses''', press '''Enter'''.
+
| Ha ka prompt, type: '''mrna equal to cdna dot transcribe open and close parentheses''', nion '''Enter'''  
−
(Ha ka prompt, thoh : '''mrna equal to cdna dot transcribe open and close parentheses''', nion '''Enter''')
+
  
 
|-
 
|-
−
|  05:55
+
|  05:55  
−
| For the output, type: ''' mrna.''' Press '''Enter'''.
+
| Na ka bynta ka output, type: ''' mrna.''' Nion '''Enter'''  
−
(Na ka bynta ka output, thoh : ''' mrna.''' Nion '''Enter''')
+
  
 
|-
 
|-
 
|  06:01
 
|  06:01
−
|Observe the output.The '''transcribe''' method replaces the '''Thiamin''' in the '''DNA''' sequence by '''Uracil'''.
+
|Khmih thuh ia ka output. Ka rukom '''transcribe''' kan bujli ia ka '''Thiamin''' ha ka '''DNA''' sequence da ka '''Uracil'''
−
(Peit  ia ka output. Ka rukom '''transcribe''' kan bujli ia ka '''Thiamin''' ha ka '''DNA''' sekwen  da ka '''Uracil''')
+
  
 
|-
 
|-
−
| 06:09
+
| 06:09  
−
|Next, to '''translate''' this '''mRNA''' to corresponding '''protein''' sequence, use the '''translate''' method.
+
|Kaba bud, ban '''translate''' ia kane ka '''mRNA''' sha ka corresponding '''protein''' sequence pyndonkam da ka rukom jong ka '''translate'''
−
(Hadien , ban '''translate''' ia kane ka '''mRNA''' sha ka corresponding '''protein''' sekwen , pyndonkam da ka rukom jong ka '''translate''')
+
  
 
|-
 
|-
−
| 06:16
+
| 06:16  
−
|Type the following code:  '''protein equal to mrna dot translate open and close parentheses'''. Press '''Enter'''.
+
| Type ia kine ki code harum: '''protein equal to mrna dot translate open and close parentheses'''. Nion '''Enter'''
−
(Thoh  ia kine ki code : '''protein equal to mrna dot translate open and close parentheses'''. Nion '''Enter''')
+
  
 
|-
 
|-
−
|  06:27
+
|  06:27
−
| The '''translate''' method translates '''RNA''' or '''DNA''' sequence using the standard genetic code, if unspecified.
+
|Ka translate method '''RNA''' lane '''DNA''' sequence da kaba pyndom ia ka standard genetic code
−
(Ka rukom '''translate'''  kan translate  '''RNA''' lane '''DNA''' sekwen  da kaba pyndom ia ka standard genetic code)
+
  
 
|-
 
|-
−
| 06:36
+
| 06:36  
−
|The output shows an amino acid sequence.
+
| Ka output ka pyni ia ka amino acid sequence.
−
(Ka output kan  pyni ia ka amino acid sekwen )
+
  
 
|-
 
|-
−
| 06:40
+
| 06:40  
−
| The output also shows information regarding the presence of '''stop codons''' in the translated sequence.
+
|Ka output ka pyni ruh ia ka thup jingtip naka bynta ka jingdon jong ka '''stop codons''' ha ka sequence lah pynkylla.
−
(Ka output kan  pyni ruh ia ka jingpyntip ia  ka jingdon jong ka '''stop codons''' ha ka sekwen  ba lah pykylla (translate)
+
  
 
|-
 
|-
−
| 06:47
+
| 06:47  
−
| Observe the asterisk at the end of the protein sequence. It indicates the '''stop codon'''.
+
|Khmih thuh ia u asterisk ha kaba kut jong ka protein sequence. U kdew ia ka '''stop codon'''.
−
(Peit  ia u asterisk ha kaba kut jong ka protein sekwen . Ka pyni  ia ka '''stop codon'''.)
+
  
 
|-
 
|-
 
| 06:53  
 
| 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'''
−
(Ha u code ba ha jrong, ngi lah pyndonkam ia u coding '''DNA''' strand na ka bynta ka '''transcription''')
+
 
    
 
    
 
|-
 
|-
 
| 06:59
 
| 06:59
−
|In Biopython, '''transcribe''' method works only on coding DNA strand.
+
| Ha Biopython, ka '''transcribe'''method ka treikam tang ha ka coding DNA strand  
−
(Ha Biopython, ka '''transcribe'''method ka treikam tang ha ka coding DNA strand)
+
 
 
|-
 
|-
 
| 07:04
 
| 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 iaid jong ka '''transcription''' ka sdang da ka '''template strand'''
−
(Hynrei, ha ka biological system ba shisha, ka rukom long  jong ka '''transcription''' ka sdang da ka '''template strand''')
+
  
 
|-
 
|-
−
| 07:11
+
| 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.
−
(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
+
| 07:20  
−
|Follow the rest of the code as shown above, for the coding strand.
+
|Bud ïaki code ba dang sah kumba lah pyni hajrong, na ka bynta ka coding strand  
−
(Leh ia kiba sah ki code  kumba lah pyni hajrong, na ka bynta ka coding strand)
+
  
 
|-
 
|-
 
| 07:24  
 
| 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 ia ka '''DNA''' sequence sha ka '''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
 
| 07:31
−
|'''DNA''' sequence of any size can be translated to a protein sequence using this code.
+
| Ka '''DNA''' sequence kaba ha kano kano ka size lah ban pynkylla sha ka protein sequence da kaba pyndonkam da une u 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
+
|  07:37  
−
|Let's summarize.In this tutorial, we have learnt:
+
|To ngin batai lyngkot. Ha kane ka tutorial, ngi pule shaphang:
−
(To ngin ia pynkut . Ha kane ka nuksa , ngi leh  shaphang:)
+
  
 
|-
 
|-
 
| 07:41
 
| 07:41
−
| Important features of '''Biopython'''
+
| Ki jinglong ba kongsan jong ka '''Biopython'''
−
(Ki mat ba donkam  ka '''Biopython''')
+
  
 
|-
 
|-
 
| 07:43
 
| 07:43
−
| Information regarding download and installation on '''Linux OS'''
+
| Ka thup jingtip shaphang ka download bad installation ha '''Linux OS'''
−
(Jingpyntip  shaphang ka download bad installation ha '''Linux OS''')
+
 
 
|-
 
|-
 
| 07:48
 
| 07:48
−
| Create a sequence object for the given '''DNA''' strand.
+
| Ban shna sequence object na ka bynta ka '''DNA''' strand
−
(Ban shna sekwen  object na ka bynta ka '''DNA''' strand)
+
  
 
|-
 
|-
 
| 07:52
 
| 07:52
−
| '''Transcription''' of the DNA sequence to '''mRNA'''.
+
| '''Transcription''' ia ka DNA sequence sha ka '''mRNA'''
−
('''Transcription''' jong ka  DNA sekwen  sha ka '''mRNA''')
+
 
 
|-
 
|-
 
| 07:56
 
| 07:56
−
| '''Translation''' of '''mRNA''' to protein sequence.
+
| '''Translation''' ia ka '''mRNA''' sha ka protein sequence.
−
('''Translation''' jong ka '''mRNA''' sha ka protein sekwen )
+
  
 
|-
 
|-
 
| 08:00
 
| 08:00
−
|Now, for the assignment-
+
| Mynta, na ka bynta ka assignment
−
(Mynta, na ka bynta ki kam )
+
  
 
|-
 
|-
−
| 08:02
+
| 08:02  
−
|Translate the given '''DNA''' sequence into '''protein''' sequence.
+
|Pynkylla ka '''DNA''' sequence ba lah ai sha ka '''protein''' sequence.
−
(Pynkylla ka '''DNA''' sekwen  ba lah ai sha ka '''protein''' sekwen )
+
  
 
|-
 
|-
 
| 08:06
 
| 08:06
−
|Observe the output.
+
| Khmih thuh ia ka output
−
(Peit  ia ka output)
+
  
 
|-
 
|-
−
|  08:08
+
|  08:08  
−
|The protein sequence has an internal '''stop codon'''.
+
|Ka protein sequence ka don ia ka '''stop codon'''
−
(Ka protein sekwen  ka don lypa  ka '''stop codon''')
+
  
 
|-
 
|-
−
| 08:11
+
| 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 U '''stop codon'''uba nyngkong haka frame
−
(Kumba ka ju long shisha, pynkylla ia ka '''DNA''' shaduh kaba nyngkong ka frame '''stop codon''') 
+
  
 
|-
 
|-
 
| 08:17
 
| 08:17
−
|Your completed assignment should have the following code.
+
| Ka assignment ba lah dep jong phi ka dei ban don ki code kiba harum  
−
(Ka kam  ba lah dep jong phi ka dei ban don ki code kiba harum)
+
  
 
|-
 
|-
−
| 08:20
+
| 08:20  
−
|Notice that we have used '''to underscore stop''' argument in the '''translate()''' method. Notice the output.
+
|Peit thuh ba ngi lah pyndonkam ka argument'''to underscore stop'''  ha ka '''translate''' method. Peit ka output
−
(To khmih bha  ba ngi lah pyndonkam ka rukom  (argument)'''to underscore stop'''  ha ka '''translate()''' method. Peit ka output)
+
 
 
|-
 
|-
 
| 08:27
 
| 08:27
−
|The '''stop codon''' itself is not translated.
+
| Ia u '''stop codon''' hi khlem shym la pynkylla
−
(U  '''stop codon''' marwei khlem shah  pynkylla)
+
  
 
|-
 
|-
 
| 08:31
 
| 08:31
−
|The stop symbol is not included at the end of your '''protein''' sequence.
+
| U stop symbol u khlem shah kynthup ha kaba kut ka '''protein''' sequence.
−
(U symbol sangeh  u khlem shah kynthup ha kaba kut ka '''protein''' sekwen )
+
  
 
|-
 
|-
 
| 08:36
 
| 08:36
−
|This video summarizes the Spoken Tutorial project.
+
| Kane ka video ka batai lyngkot ia ka Spoken Tutorial project  
−
(Kane ka video ka lum kyllum  ia ka Spoken Tutorial project)
+
  
 
|-
 
|-
 
| 08:39
 
| 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  
−
(Lada phim don ka bandwidth ba bha, phi lah ban download bad peit ia ka)
+
  
 
|-
 
|-
−
|08:43
+
|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 pynlong workshop bad ai certificates sha kito ba pass ia ka 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
 
| 08:50
−
|For more details, please write to us.
+
| Ban tip kham bniah, sngewbha thoh sha ngi
−
(Ban tip kham bniah, sngewbha thoh sha ngi)
+
  
 
|-
 
|-
 
| 08:53
 
| 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
−
(Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Government of India)
+
  
 
|-
 
|-
−
| 08:59  
+
| 08:59
−
|More information on this mission is available at this link.
+
|  Khambuh ki jingtip halor kane ka mission ka don ha kane ka link
−
(Na ka bynta ki jingtip ba kham pura jong  kane ka mission phin lap  ha kane ka link)
+
  
 
|-
 
|-
−
| 09:03
+
| 09:03  
−
|This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.
+
|ïa kane ka script la pynkylla sha ka Ktien Khasi da i Yuwanki Yolande Kharlukhi na Shillong, khublei ba phi la ïasnoh lang.
−
(Ha kaba kut, Nga dei ka Snehalatha na '''IIT Bombay'''. Khublei shibun
+
−
|}
+

Latest revision as of 11:10, 29 May 2018

Time Narration
00:01 Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka Introduction to Biopython.
00:05 Ha kane ka tutorial, ngin ia pule shaphang ki jingling ba kongsan jong ka Biopython
00:10 Ki jingpyntip shaphang ban download bad ban install ha ka Linux Operating System
00:15 Bad ka translation ia ka DNA sequence sha ka protein sequence pyndonkam da ki tiar ka Biopython
00:22 Ban bud ia kane ka tutorial, phi dei ban tip bha ia ka
00:25 Undergraduate Biochemistry lane Bioinformatics
00:29 bad ka basic Python programming
00:31 Peit ia ki Python' tutorial ha ka link bala ai
00:35 Ban record ia kane ka tutorial, nga pyndonkam da ka * Ubuntu OS version 12.04
00:41 Python version 2.7.3
00:44 Ipython version 0.12.1 bad
00:48 Biopython version 1.58.
00:51 Ka Biopython ka dei ka jinglum kyllum ia ki modules na ka bynta ka computational biology
00:57 ka lah ban trei ia kiba suk eh haduh kiba khia tam ki kam kiba donkam ha ka bioinformatics
01:03 Ia ki tiar jong ka Biopython lah ju pyndonkam na ka bynta
01:05 Parsing, kata kaba mut ba wad jingtip na kiba bun ki file formats kum ka FASTA, Genbank, bad kumta ter ter
01:14 Ban download data na ka database websites kum ka NCBI, ExPASY, bad kumta ter ter
01:22 Ban Run ïaki Bioinformatic algorithms kum ka BLAST.
01:26 Ka don ia ki tools ban trei ki kam ha ka rukom ba ryntih
01:31 Kum ka nuksa – ban ioh complements, transcription, translation bad kumta ter ter
01:38 Ki code ban peit ia ka alignment
01:40 bad ki code ban phiah ia ki kam ha ki bynta ba pher ba pher
01:46 Jingpyntip shaphang ban download
01:48 Ka Biopython kam dei kaba wan lang bad ka Python; ngi hap ban download ïaka laka jong
01:54 Ban tip kham bniah, peit ia ka link ba harum.
01:59 Ban install ha ka system Linux
02:02 Install ia ka Python, Ipython bad Biopythonda kaba pyndonkam da ka Synaptic Package Manager
02:08 Ki software ba donkam kin sa install hi
02:13 Ngi hap ban install hi ia ki software jong ka graphic outputs bad plots
02:18 Plie ia ka terminal da kaba nion lang ia u Ctrl, Alt bad T key
02:24 Nga lah dep install lypa ia ka Python, Ipython bad Biopython ha system jong nga
02:30 Plie ia ka Ipython interpreter da kaba type "ipython" bad sa nion Enter
02:35 Ka IPythonprompt ka paw ha screen
02:38 Ban pyntikna ba lah install ia kaBiopython, ha ka prompt, type "import Bio", bad sa press Enter
02:48 Lada phim ioh message error ei ei, ka mut ka Biopython lah install
02:54 Hangne, to ngan pynkynmaw ia phi ba kaPython language ka long case sensitive
02:59 Da phikir bha haba type ki keywords, ki variables lane functions
03:04 Kumba long, u lain haneng, u, “i” ha import dei u lowercase bad u “B”dei u uppercase ha Bio
03:12 Ha kane ka tutorial, ngin pyndonkam da ka Biopythonmodules ban pynkylla ia ka DNA sequence
03:19 Ki rukom pyndonkam ki long harum
03:22 Nyngkong eh, shna ia ka sequence object ban code ia ka DNA strand
03:27 Nangta, sa ka transcription ban code ia ka DNA strand sha ka mRNA
03:32 Khatduh eh, translation jong ka mRNA sha ka protein sequence.
03:37 Ngin pyndonkam da ka coding DNA strand kumba lah pyni ha ka slide, kum ka nuksa
03:42 Ka code naka bynta u protein sequence barit
03:46 ka synjam ba nyngkong ka dei ban shna ia ka sequence object na ka bynta ka coding DNA strand kaba hajrong
03:52 To ngin ia phai biang sha ka terminal
03:55 Ban shna ia ka sequence object, import ïaka ka Seq module na ka Bio package
04:02 Ka Seq module ka ai iaki rukom ban pyllang bad ban shna ia ki sequence objects
04:08 Ha ka prompt, type: from Bio dot Seq import Seq bad sa nion Enter
04:17 Nangta, batai shai ia ki alphabets ha ka strand, haba shna ia ka sequence object jong phi.
04:24 Kata ban thikna lada ia ka sequence jong ki alphabets code na ka bynta ka nucleotides lane amino acids
04:32 Ban leh kumta, ngin pyndonkam da ka IUPAC module na ka Alphabet package
04:38 Ha ka prompt, type: from Bio dot Alphabet import IUPAC. Sa nion Enter
04:48 Kynmaw ba ngi lah pyndonkam import bad from statements ban load "Seq" bad "IUPAC" modules
04:56 Buh ia u sequence object ha ka variable kaba kyrteng cdna
05:01 Ha ka prompt, type: cdna equal to Seq kum ha ki normal string
05:08 Pyndait ia ki sequence hapoh ki double quotes bad parentheses
05:13 Ngi tip ba ka sequence jong ngi ka dei ka DNA ba lyngkhot. Te, type unambiguous DNA alphabet object kum ka argument
05:21 Na ka bynta ka output, type: cdna. Nion Enter
05:26 Ka output ka pyni ia ka DNA sequence kum ka sequence object
05:30 To ngin thoh ia ka coding DNA strand sha ka mRNA. Ba ïadei bad kane.
05:35 Ngin pyndonkam da ka rukom Seq module's built-in “transcribe”
05:39 Type ia ki code kiba harum
05:41 Buh ia ka output ha ka variable mrna
05:45 Ha ka prompt, type: mrna equal to cdna dot transcribe open and close parentheses, nion Enter
05:55 Na ka bynta ka output, type: mrna. Nion Enter
06:01 Khmih thuh ia ka output. Ka rukom transcribe kan bujli ia ka Thiamin ha ka DNA sequence da ka Uracil
06:09 Kaba bud, ban translate ia kane ka mRNA sha ka corresponding protein sequence pyndonkam da ka rukom jong ka translate
06:16 Type ia kine ki code harum: protein equal to mrna dot translate open and close parentheses. Nion Enter
06:27 Ka translate method RNA lane DNA sequence da kaba pyndom ia ka standard genetic code
06:36 Ka output ka pyni ia ka amino acid sequence.
06:40 Ka output ka pyni ruh ia ka thup jingtip naka bynta ka jingdon jong ka stop codons ha ka sequence lah pynkylla.
06:47 Khmih thuh ia u asterisk ha kaba kut jong ka protein sequence. U kdew ia ka stop codon.
06:53 Ha u code ba ha jrong, ngi lah pyndonkam ia u coding DNA strand na ka bynta ka transcription
06:59 Ha Biopython, ka transcribemethod ka treikam tang ha ka coding DNA strand
07:04 Hynrei, ha ka biological system ba shisha, ka rukom iaid jong ka transcription ka sdang da ka template strand
07:11 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 Bud ïaki code ba dang sah kumba lah pyni hajrong, na ka bynta ka coding strand
07:24 Da kaba pyndonkam da ki rukom ha Biopython ngi la dep ban pynkylla ia ka DNA sequence sha ka protein sequence.
07:31 Ka DNA sequence kaba ha kano kano ka size lah ban pynkylla sha ka protein sequence da kaba pyndonkam da une u code
07:37 To ngin batai lyngkot. Ha kane ka tutorial, ngi pule shaphang:
07:41 Ki jinglong ba kongsan jong ka Biopython
07:43 Ka thup jingtip shaphang ka download bad installation ha Linux OS
07:48 Ban shna sequence object na ka bynta ka DNA strand
07:52 Transcription ia ka DNA sequence sha ka mRNA
07:56 Translation ia ka mRNA sha ka protein sequence.
08:00 Mynta, na ka bynta ka assignment
08:02 Pynkylla ka DNA sequence ba lah ai sha ka protein sequence.
08:06 Khmih thuh ia ka output
08:08 Ka protein sequence ka don ia ka stop codon
08:11 Kumba ka ju long shisha, pynkylla ia ka DNA shaduh U stop codonuba nyngkong haka frame
08:17 Ka assignment ba lah dep jong phi ka dei ban don ki code kiba harum
08:20 Peit thuh ba ngi lah pyndonkam ka argumentto underscore stop ha ka translate method. Peit ka output
08:27 Ia u stop codon hi khlem shym la pynkylla
08:31 U stop symbol u khlem shah kynthup ha kaba kut ka protein sequence.
08:36 Kane ka video ka batai lyngkot ia ka Spoken Tutorial project
08:39 Lada phim don ka bandwidth ba bha, phi lah ban download bad peit ia ka
08:43 Ka Spoken Tutorial Project team ka pynlong workshop bad ai certificates sha kito ba pass ia ka online test
08:50 Ban tip kham bniah, sngewbha thoh sha ngi
08:53 Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Government of India
08:59 Khambuh ki jingtip halor kane ka mission ka don ha kane ka link
09:03 ïa kane ka script la pynkylla sha ka Ktien Khasi da i Yuwanki Yolande Kharlukhi na Shillong, khublei ba phi la ïasnoh lang.

Contributors and Content Editors

Hezekiah2016

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