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

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{| Border=1
+
{| border=1
! <center>Time</center>
+
| '''Time'''
! <center>Narration</center>
+
| '''Narration'''
 
+
|-
+
|  00:01
+
|Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka '''Introduction to Biopython'''.
+
  
 +
|-
 +
|00:01
 +
| Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka '''Introduction to Biopython'''.
  
 
|-
 
|-
| 00:05
+
|00:05  
|Ha kane ka tutorial , ngin pule shaphang ki jinglong ba kongsan jong ka '''Biopython'''
+
|Ha kane ka tutorial, ngin ia pule shaphang ki jingling ba kongsan 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