Difference between revisions of "Biopython/C2/Manipulating-Sequences/Khasi"

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(Created page with "{| Border=1 |'''Time''' |'''Narration''' |- | 00:01 | Welcome to this tutorial on '''Manipulating Sequences.''' (Ngi pdiang sngewbha ia phi sha kane ka tutorial jong ka '''M...")
 
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| 00:01
+
| 00:01 Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka '''Manipulating Sequences.'''
| Welcome to this tutorial on '''Manipulating Sequences.'''
+
(Ngi pdiang sngewbha ia phi sha kane ka tutorial jong  ka '''Manipulating Sequences.''')
+
  
  
 
|-
 
|-
| 00:06
+
| 00:06   Ha kane ka tutorial, ngin pyndonkam ki tools ka '''Biopython''': Ban pynmih ia u random DNA sequence
| In this tutorial, we will use '''Biopython''' tools: To generate a random DNA sequence
+
(Ha kane ka tutorial, ngin pyndonkam ki tools ka '''Biopython''': Ban pynmih ia u random DNA sequence)
+
  
 
|-
 
|-
 
| 00:13
 
| 00:13
| Slice a DNA sequence at specified locations
+
  Phiah ia u DNA sequence ha ki jaka ba lah buh
(Phiah ia u DNA sequence ha ki jaka ba lah bynshet )
+
  
 
|-
 
|-
 
| 00:17
 
| 00:17
| Join two sequences together to form a new sequence that is to concatenate
+
  Pyndait lang ia artylli ki sequences ban pynlong kawei ka sequence ba thymmai
(Pyndait lang ia artylli ki sequences ban pynlong kawei ka sequence ba thymmai)
+
  
 
|-
 
|-
 
| 00:22
 
| 00:22
| Find the length of the sequence
+
  Wad ia ka jingjrong jong ka sequence
(Wad ia ka jingjrong jong ka sequence)
+
  
 
|-
 
|-
 
| 00:26
 
| 00:26
| Count the number of individual '''base'''s or part of the '''string'''
+
    Niew ia ki number jong ki  '''base''' lane ki dkhot jong u '''string'''
( Niew ia ki number jong ki  '''base''' lane ki dkhot jong u '''string''')
+
  
 
|-
 
|-
 
| 00:31
 
| 00:31
| Find a particular base or part of the string.
+
  Wad ia u base ba la thmu lane bynta jong u string
(Wad ia u base uba bniah  lane bynta jong u string)
+
  
 
|-
 
|-
 
| 00:35
 
| 00:35
| Convert a '''sequence object''' to a mutable sequence object.
+
  Pynkylla ia ka '''sequence object''' sha ka mutable sequence object
(Pynkylla ia ka '''sequence object''' sha ka mutable sequence object)
+
  
 
|-
 
|-
 
| 00:40
 
| 00:40
| To follow this tutorial, you should be familiar with undergraduate Biochemistry or Bioinformatics
+
  Ban bud ia kane ka tutorial, phi dei ban tip bha ia ka undergraduate Biochemistry lane Bioinformatics
(Ban sngewthuh  ia kane ka tutorial, phi dei ban long kiba shemphang ha  ka undergraduate Biochemistry lane Bioinformatics)
+
  
 
|-
 
|-
 
| 00:47
 
| 00:47
|and basic Python programming.
+
  Bad ka basic Python programming
(Bad ka basic Python programming)
+
  
 
|-
 
|-
 
|  00:51
 
|  00:51
|If not, refer to the '''Python''' tutorials at the given link.
+
Lada em, peit ia ki tutorials '''Python''' ha ka link ba la ai
(lem kumta, pyndonkam da ka nuksa  '''Python''' ha ka link ba bud )
+
  
 
|-
 
|-
 
| 00:56
 
| 00:56
| To record this tutorial, I am using: * '''Ubuntu OS''' version 14.10
+
  Ban record ia kane ka tutorial, nga pyndonkam da ka * '''Ubuntu OS''' version 14.10
(Ban record ia kane ka nuksa , nga pyndonkam da ka * '''Ubuntu OS''' version 14.10)
+
  
 
|-
 
|-
 
| 01:03
 
| 01:03
| '''Python''' version 2.7.8
+
  '''Python''' version 2.7.8
('''Python''' version 2.7.8)
+
  
 
|-
 
|-
 
| 01:07
 
| 01:07
| '''Ipython interpreter''' version 2.3.0
+
  '''Ipython interpreter''' version 2.3.0
('''Ipython interpreter''' version 2.3.0)
+
  
 
|-
 
|-
 
| 01:12
 
| 01:12
|'''Biopython''' version 1.64.
+
  '''Biopython''' version 1.64.
('''Biopython''' version 1.64.)
+
  
 
|-
 
|-
 
| 01:16
 
| 01:16
|Let me open the '''terminal''' and start '''ipython interpreter'''.
+
  To ngin ia plie iaka '''terminal''' bad sdang ia ka '''ipython interpreter'''
(To ngin ia plie iaka '''terminal''' bad sdang ia ka '''ipython interpreter''')
+
  
 
|-
 
|-
 
| 01:21
 
| 01:21
|Press '''Ctrl, Alt''' and '''t''' keys simultaneously.
+
  Nion lang ia u '''Ctrl, Alt''' and '''t''' key
(Nion sah  ia u '''Ctrl, Alt''' and '''t''' key)
+
  
 
|-
 
|-
 
|01:26
 
|01:26
|At the prompt, type: "ipython" and press '''Enter'''.
+
  Ha ka prompt, type: "ipython" bad sa nion '''Enter'''
(Ha ka prompt, type: "ipython" bad sa nion '''Enter''')
+
  
 
|-
 
|-
 
| 01:31
 
| 01:31
|'''Ipython''' prompt appears on the screen.
+
  Ka '''Ipython''' prompt kan sa mih ha ka screen
(Ka '''Ipython''' prompt kan sa mih ha ka screen)
+
  
 
|-
 
|-
 
| 01:35
 
| 01:35
|Using Biopython, we can generate a '''sequence object''' for a random DNA sequence of any specified length.
+
  Da kaba pyndonkam ia ka Biopython, ngi lah ban pynmih ia ka '''sequence object''' na ka bynta ka random DNA sequence ha kano kano ka jingjrong   
(Da kaba pyndonkam ia ka Biopython, ngi lah ban pynmih ia ka '''sequence object''' na ka bynta ka random DNA sequence ha kano kano ka jingjrong)  
+
  
 
|-
 
|-
 
| 01:44
 
| 01:44
|Let us now generate a sequence object for a DNA sequence of 20 bases.
+
  To mynta ngin ia pynmih ia ka sequence object na ka bynta ka DNA sequence kaba 20 bases
(To ngin ia pynmih ia ka sequence object na ka bynta ka DNA sequence kaba 20 bases)
+
  
 
|-
 
|-
 
|01:50
 
|01:50
|At the prompt, type: "import random", press '''Enter'''.
+
  Ha ka prompt, type: "import random", bad nion '''Enter'''.
(Ha ka prompt, type: "import random", bad nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 01:56
 
| 01:56
| Next, import '''Seq '''module from '''Bio '''package.
+
  Nangta, import '''Seq '''module na '''Bio '''package.
(Nangta, import '''Seq '''module na '''Bio '''package.)
+
  
 
|-
 
|-
 
| 02:01
 
| 02:01
|Often '''Seq''' is pronounced as '''seek'''.
+
  Bunsien '''Seq''' ngi ju pronounce kum '''seek'''.
(Barabor  '''Seq''' ngi shait ong  '''seek'''.)
+
  
 
|-
 
|-
 
| 02:06
 
| 02:06
| At the prompt, type: '''From Bio dot Seq import Seq'''. Press '''Enter'''.
+
  Ha ka prompt, type: '''From Bio dot Seq import Seq'''. Nion '''Enter'''.
(Ha ka prompt, type: '''From Bio dot Seq import Seq'''. Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 02:15
 
| 02:15
| We will use '''Bio.Alphabet''' module to specify the alphabets in the DNA sequence.
+
  Ngin pyndonkam da ka '''Bio.Alphabet''' module ban pyntikna ia ki alphabets ha ka DNA sequence
(Ngin pyndonkam da ka '''Bio.Alphabet''' module ban pyntikna ia ki alphabets ha ka DNA sequence)
+
  
 
|-
 
|-
 
| 02:22
 
| 02:22
| Type: '''from Bio dot Alphabet import generic underscore dna.''' Press '''Enter'''.
+
  Type: '''from Bio dot Alphabet import generic underscore dna.''' Nion '''Enter'''.
(Type: '''from Bio dot Alphabet import generic underscore dna.''' Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 02:32
 
| 02:32
| Type the following '''command''' to create a sequence object for the random DNA sequence.
+
  Type ia ki '''command''' harum ban shna ia ka sequence object na ka bynta ka randon DNA sequence.  
(Type kumne harum '''command''' ban shna ia ka sequence object na ka bynta ka DNA sequence. )
+
  
 
|-
 
|-
 
| 02:38
 
| 02:38
|Store the sequence in a variable '''dna1'''.
+
  Buh ia ka sequence ha ka variable '''dna1'''
(Pynlang  ia ka sequence ha ka variable '''dna1''')
+
  
 
|-
 
|-
 
| 02:42
 
| 02:42
|Please note: in this command, use two single quotes instead of a double quote. Press '''Enter'''.
+
  Sngewbha peit: ha kane ka command, pyndonkam ar tylli ki single quotes ha ka jaka ka double quote. Nion '''Enter'''
(Sngewbha peit: ha kane ka command, pyndonkam ar tylli ki single quotes ha ka jaka ka double quote. Nion '''Enter''')
+
  
 
|-
 
|-
 
| 02:50
 
| 02:50
| For the output, type: '''dna1'''. Press '''Enter'''.
+
  Na ka bynta ka output, type: '''dna1'''. Nion '''Enter'''
(Na ka bynta ka output, type: '''dna1'''. Nion '''Enter''')
+
  
 
|-
 
|-
 
| 02:55
 
| 02:55
|  The output shows the '''sequence object''' for the random DNA sequence.
+
  Ka output ka pyni ia ka '''sequence object''' na ka bynta ka random DNA sequence.  
(Ka output ka pyni ia ka '''sequence object''' na ka bynta ka random DNA sequence. )
+
  
 
|-
 
|-
 
| 03:00
 
| 03:00
| If you want a new sequence, press up-arrow key to get the same command as above. Press '''Enter'''.
+
  Lada phi kwah ka sequence ba thymmai, nion u up-arrow key ban ioh ia ka juh ka command kum haneng. Nion '''Enter'''.  
(Lada phi kwah ka sequence ba thymmai, nion u up-arrow key ban ioh ia ka juh ka command kum haneng. Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 03:11
 
| 03:11
|For the output, type the variable name '''dna1.''' Press '''Enter'''.
+
  Na ka bynta ka output, type ia ka kyrteng ka variable '''dna1.''' Nion '''Enter'''
(Na ka bynta ka output, type ia ka kyrteng ka variable '''dna1.''' Nion '''Enter''')
+
  
 
|-
 
|-
 
| 03:17
 
| 03:17
| The output shows a new DNA sequence which is different from the first one.
+
  Ka output ka pyni iaka DNA sequence ba thymmai kaba pher na kaba nyngkong.
(Ka output ka pyni iaka DNA sequence ba thymmai kaba pher na kaba nyngkong.)
+
  
 
|-
 
|-
 
| 03:23
 
| 03:23
|  About '''Sequence Objects''':
+
  Shaphang ka '''Sequence Objects'''
(Shaphang ka '''Sequence Objects''')
+
  
 
|-
 
|-
 
| 03:25
 
| 03:25
|The '''sequence objects''' usually act like normal '''Python string'''s.
+
  Ka '''sequence objects''' ha ka jingshisha ka long kum ka '''Python string'''s.
(Ka '''sequence objects''' ha ka jingshisha ka long beit  '''Python string'''s.)
+
  
 
|-
 
|-
 
| 03:30
 
| 03:30
|So, follow the normal conventions as you do for Python strings.
+
  Te, bud beit ia ka rukom leh kumba leh ia ka Python strings.
(Te, bud beit ia ka rukom leh kumba leh ia ka Python strings.)
+
  
 
|-
 
|-
 
| 03:35
 
| 03:35
|In Python, we count the characters in the string starting from 0, instead of 1.
+
  Ha ka Python, ngi niew ia ki characters ha ka string kaba sdang na 0, ha jaka u 1.
(Ha ka Python, ngi niew ia ki characters ha ka string kaba sdang na 0, ha jaka u 1.)
+
  
 
|-
 
|-
 
| 03:41
 
| 03:41
|The first character in the sequence is position zero.
+
  U character ba nyngkong ha ka sequence u dei u zero.
(U character ba nyngkong ha ka sequence u dei u zero.)
+
  
 
|-
 
|-
 
| 03:45
 
| 03:45
| Back to the terminal.
+
  Phai biang sha ka terminal.
(Phai biang sha ka terminal.)
+
  
 
|-
 
|-
 
| 03:47
 
| 03:47
|Often you may need to work with only a part of the sequence.
+
  Teng teng ngi hap ban trei tang shi bynta jong ka sequence
(Teng teng ngi hap ban trei tang shi bynta jong ka sequence)
+
  
 
|-
 
|-
 
| 03:52
 
| 03:52
|Now, let's see how to extract parts of the string and store them as sequence objects.
+
  Mynta, ngin ia peit kumno ban sei ia ki bynta jong ka string bad buh ia ki kum ki sequence objects.
(Mynta, ngin ia peit kumno ban sei ia ki dkhot  jong ka string bad buh ia ki kum ki sequence objects.)
+
  
 
|-
 
|-
 
| 03:58
 
| 03:58
|For example, we will '''slice''' the DNA sequence at two positions.
+
  Nuksa, ngin '''slice''' ia ka DNA sequence ha ki ar bynta.
(Nuksa, ngin '''slice''' ia ka DNA sequence ha ki ar bynta.)
+
  
 
|-
 
|-
 
| 04:04
 
| 04:04
|First, between bases 6 and 7.
+
  Nyngkong, hapdeng ki bases 6 bad 7.
(Nyngkong, hapdeng ki bases 6 bad 7.)
+
  
 
|-
 
|-
 
| 04:08
 
| 04:08
|This will extract a fragment from the beginning of the sequence to the 6th base in the sequence.
+
  Kane kan sei ia ka fragment na kaba sdang jong ka sequence sha ka base ba 6 ha ka sequence.
(Kane kan sei ia ka fragment na kaba sdang jong ka sequence sha ka base ba 6 ha ka sequence.)
+
  
 
|-
 
|-
 
| 04:15
 
| 04:15
|  The second slice will be between bases 11 and 12.
+
  Ka slice ba ar kan dei hapdeng ka bases 11 bad 12.
(Ka slice ba ar kan dei hapdeng ka bases 11 bad 12.)
+
  
 
|-
 
|-
 
| 04:20
 
| 04:20
|The second fragment will be from the 12th base to the end of the sequence.
+
  Ka fragment ba ar kan dei na ka base ba 12 shaduh ba kut jong ka sequence.
(Ka fragment ba ar kan dei na ka base ba 12 shaduh ba kut jong ka sequence.)
+
  
 
|-
 
|-
 
| 04:26
 
| 04:26
| Type the following command, at the prompt, to extract the first fragment.
+
  Type ia ka command ba harum, ha ka prompt, ban sei ia ka fragment ba nyngkong.  
(Type ia ka command ba harum, ha ka prompt, ban sei ia ka fragment ba nyngkong.)
+
  
 
|-
 
|-
 
| 04:31
 
| 04:31
|'''String1 equal to dna1 within brackets 0 colon 6.'''
+
  '''String1 equal to dna1 within brackets 0 semi-colon 6.'''
('''String1 equal to dna1 within brackets 0 colon 6.''')
+
  
 
|-
 
|-
 
| 04:39
 
| 04:39
|'''string1''' is the variable to store the first fragment.
+
  '''string1''' ka dei ka variable ban lum ia ka fragment ba nyngkong.
('''string1''' ka dei ka variable ban lum ia ka fragment ba nyngkong.)
+
  
 
|-
 
|-
 
| 04:43
 
| 04:43
|The rest of the command follows as in normal Python.
+
  Ki command ba bud kin long beit kum ha ka Python.
(Ki command ba bud kin long beit kum ha ka Python.)
+
  
 
|-
 
|-
 
| 04:47
 
| 04:47
|Enclosed in these brackets are the start and the stop positions separated by a colon.
+
  Hapoh kine ki brackets dei ki jaka ba sdang bad ba sangeh ba ba la pyniakhlad da u colon.
(Hapoh kine ki brackets dei ki jaka ba sdang bad ba kut  ba shah phiah  da u colon.)
+
  
 
|-
 
|-
 
| 04:53
 
| 04:53
|The positions are inclusive of the start but exclusive of the stop position. Press '''Enter'''.
+
  Kine ki jaka ki kynthup lang ia kaba sdang hynrei khlem kynthup ïaki ha ka jaka ba sangeh. Nion '''Enter'''.
(Kine ki jaka (positions)  ki lum lang ha  kaba sdang hynrei kim shah lum shuh ha kaba kut  . Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 05:01
 
| 05:01
| To view the output, type: "string1", press '''Enter'''.
+
  Ban peit ia ka output, type: "string1", nion '''Enter'''.
(Ban peit ia ka output, type: "string1", nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 05:04
 
| 05:04
|The output shows the first fragment as the sequence object.
+
  Ka output ka pyni ia ka fragment ba nyngkong kum ka sequence object.
(Ka output ka pyni ia ka fragment ba nyngkong kum ka sequence object.)
+
  
 
|-
 
|-
 
| 05:10
 
| 05:10
| To extract the second string from the sequence, press up-arrow key and '''edit''' the command as follows:
+
  Ban sei ia ka string ba ar na ka sequence, nion ia u up-arrow key bad '''edit''' ia ka command kumne harum:  
(Ban sei ia ka string ba ar na ka sequence, nion ia u up-arrow key bad '''edit''' ia ka command kumne harum: )
+
  
 
|-
 
|-
 
| 05:17
 
| 05:17
|Change the name of the variable to '''string2''' and positions to '''11 '''and '''20'''.
+
  Pynkylla ia ka ka kyrteng jong u variable sha ka '''string2''' bad jaka sha u '''11 '''bad '''20'''.   
(Pynkylla ia ka ka kyrteng jong u variable sha ka '''string2''' bad jaka sha u '''11 '''bad '''20'''.)  
+
  
 
|-
 
|-
 
| 05:24
 
| 05:24
| For the output, type: "string2". Press '''Enter'''.
+
  Na ka bynta ka output, type: "string2". Nion '''Enter'''.
(Na ka bynta ka output, type: "string2". Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 05:30
 
| 05:30
|Now we have the 2nd fragment also as a sequence object.
+
  Mynta ngi ioh ia ka fragment ba ar ruh kum ka sequence object.
(Mynta ngi ioh ia ka fragment ba ar ruh kum ka sequence object.)
+
  
 
|-
 
|-
 
| 05:34
 
| 05:34
| Let us concatenate, that is, add the two '''strings '''together to form a new fragment.
+
  To ngin pynlong ïaki kawei, kata, ban pyndait lang ia baroh ar ki '''strings ''' ban pynlong u fragment ba thymmai.
(To ngin ia lum lang , kata, ban pyndait lang ia baroh ar ki '''strings ''' ban ioh  u fragment ba thymmai.)
+
  
 
|-
 
|-
 
| 05:42
 
| 05:42
|Store the new sequence in a variable '''dna2'''.
+
  Buh ia ka sequence ba thymmai ha ka variable '''dna2'''.
(Buh ia ka sequence ba thymmai ha ka variable '''dna2'''.)
+
  
 
|-
 
|-
 
| 05:46
 
| 05:46
|Type: '''dna2 equal to string1 plus string2'''. Press '''Enter'''.
+
  Type: '''dna2 equal to string1 plus string2'''. Nion '''Enter'''.
(Type: '''dna2 equal to string1 plus string2'''. Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 05:53
 
| 05:53
|Please note: we cannot add sequences with incompatible alphabets.
+
  Sngewbha kynmaw ba: ngim lah ban thep ki sequence da ki alphabets ki bym iahap.
(Sngewbha tip ba : ngim lah ban iasnoh ia  ki sequence bad ki alphabets ki bym iahap.)
+
  
 
|-
 
|-
 
| 05:59
 
| 05:59
|That is, we cannot concatenate a DNA sequence and a protein sequence to form a new sequence.
+
  Kata ka mut, ngim lah ban pynlong kawei ia ka DNA sequence bad ka protein sequence ban ioh ia ka sequence ba thymmai.
(Kata ka mut, ngim lah ban lum  ia ka DNA sequence bad ka protein sequence ban ioh ia ka sequence ba thymmai.)
+
  
 
|-
 
|-
 
| 06:07
 
| 06:07
|The two sequences must have the same alphabet attribute.
+
  Ki ar tylli ki sequences ki dei ban don kajuh ka alphabet attribute.
(Ki ar tylli ki sequences ki dei ban don kajuh ka alphabet attribute.)
+
  
 
|-
 
|-
 
| 06:12
 
| 06:12
| To view the output, type: "dna2". Press '''Enter'''.
+
  Ban peit ia ka output, type: "dna2". Nion '''Enter'''.
(Ban peit ia ka output, type: "dna2". Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 06:17
 
| 06:17
|The output shows a new sequence which is a combination of '''string1''' and '''string2.'''
+
  Ka output ka pyni ia ka sequence ba thymmai kaba dei ka jing pyndait lang jong u '''string1''' bad '''string2.'''
(Ka output ka pyni ia ka sequence ba thymmai kaba dei ka jinglum kyllum  jong u '''string1''' bad '''string2.''')
+
  
 
|-
 
|-
 
| 06:23
 
| 06:23
| To find the length of the new sequence, we will use '''len '''function.
+
  Ban ioh ia ka jingjrong jong ka sequence ba thymmai, ngin pyndonkam da ka '''len '''function.  
(Ban ioh ia ka jingjrong jong ka sequence ba thymmai, ngin pyndonkam da ka '''len '''function.)
+
  
 
|-
 
|-
 
| 06:29
 
| 06:29
| Type: "len" within parenthesis "dna2". Press '''Enter'''.
+
  Type: "len" hapoh parenthesis"dna2". Nion '''Enter'''.
(Type: "len" hapoh parenthesis"dna2". Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 06:34
 
| 06:34
|Output shows the sequence as 15 bases long.
+
  Ka output ka pyni ia ka sequence kaba jrong 15 bases.
(Ka output ka pyni ia ka sequence kaba jrong 15 bases.)
+
  
 
|-
 
|-
 
| 06:39
 
| 06:39
| We can also count the number of individual bases present in the sequence.
+
  Ngi lah ruh ban niew ia ka jingdon jong ki bases bapher bapher ha ka sequence.  
(Ngi lah ruh ban niew ia ka jingdon jong ki bases bapher bapher ha ka sequence.)
+
  
 
|-
 
|-
 
| 06:44
 
| 06:44
|To do so, we will use '''count()''' function.
+
  Ban leh ia kane, ngin pyndonkam da ka '''count ''' function.
(Ban leh ia kane, ngin pyndonkam da ka '''count()''' function.)
+
  
 
|-
 
|-
 
| 06:47
 
| 06:47
|For example- to count the number of alanines present in the sequence, type the following command: '''dna2 dot count''' within parenthesis within double quotes alphabet A.
+
  Kum ka nuksa – ban niew ia ka jingdon jong u alanines ba don ha ka sequence, ngi type ia ka command ka ba harum: '''dna2 dot count''' hapoh parenthesis hapoh double quotes alphabet A.  
(Nuksa  – ban niew ia ka jingdon jong u alanines ba don ha ka sequence, ngi type ia ka command ka ba harum: '''dna2 dot count''' hapoh parenthesis hapoh double quotes alphabet A. )
+
  
 
|-
 
|-
 
| 07:02
 
| 07:02
|Press '''Enter'''.
+
  Nion '''Enter'''.
(Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 07:04
 
| 07:04
|The output shows the number of alanines present in the sequence '''dna2'''.
+
  Ka output ka pyni ia ka jingdon jong u alanines ha ka sequence '''dna2'''.
(Ka output ka pyni ia ka jingdon jong u alanines ha ka sequence '''dna2'''.)
+
  
 
|-
 
|-
 
| 07:10
 
| 07:10
| To find a particular base or part of the string, we will use '''find()''' function.
+
  Ban shem ia u jait base ne u dkhot jong u string, ngin pyndonkam da u '''find ''' function.
(Ban wad  ia u jait base ne u dkhot jong u string, ngin pyndonkam da u '''find()''' function.)
+
  
 
|-
 
|-
 
| 07:16
 
| 07:16
|Type: '''dna2 dot find''' within parenthesis within double quotes "GC". Press '''Enter'''.
+
  Type: '''dna2 dot find''' hapoh parenthesis hapoh double quotes "GC". Nion '''Enter'''.
(Type: '''dna2 dot find''' hapoh parenthesis hapoh double quotes "GC". Nion '''Enter'''.)
+
 
 
|-
 
|-
 
| 07:26
 
| 07:26
|The output indicates the position of the first instance of the appearance of '''GC''' in the string.
+
  Ka output ka pyni ia ka jaka ba nyngkong kaba mih ka '''GC''' ha u string.
(Ka output ka pyni ia ka jaka ba nyngkong kaba mih ka '''GC''' ha u string.)
+
  
 
|-
 
|-
 
| 07:32
 
| 07:32
| Normally a sequence object cannot be edited.
+
  Ha ka jingshisha ia ka sequence object um ju lah ban pynkylla.
(Ha ka jingshisha ia ka sequence object um ju lah ban pynkylla.)
+
  
 
|-
 
|-
 
| 07:35
 
| 07:35
|To edit a sequence, we have to convert it to the mutable sequence object.
+
  Ban pynkylla ia ka sequence, ngi dei ban pynkylla iaka sha ka mutable sequence object.
(Ban pynkylla ia ka sequence, ngi hap  ban pynkylla sha ka mutable sequence object.)
+
  
 
|-
 
|-
 
| 07:41
 
| 07:41
|To do so, type: '''dna3 equal to dna2 dot to mutable''' open and close parenthesis. Press '''Enter'''.
+
  Ban leh ia kane, type: '''dna3 equal to dna2 dot to mutable''' plie bad khang ia u parenthesis. Nion '''Enter'''.
(Ban leh ia kane, type: '''dna3 equal to dna2 dot to mutable''' plie bad khang ia u parenthesis. Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 07:52
 
| 07:52
| For the output, type: '''dna3'''. Press '''Enter'''.
+
  Na ka bynta ka output, type: '''dna3''' Nion '''Enter'''.
(Na ka bynta ka output, type: '''dna3''' Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 07:55
 
| 07:55
| Now the sequence object can be edited.
+
  Mynta ngin sa lah ban pynkylla ia ka sequence object.
(Mynta ngin sa lah ban pynkylla ia ka sequence object.)
+
  
 
|-
 
|-
 
| 07:59
 
| 07:59
|Let us replace a '''base''' from the sequence.
+
  To ngin ia bujli ia u '''base''' na ka sequence.
(To ngin ia weng/bujli ia u '''base''' na ka sequence.)
+
  
 
|-
 
|-
 
| 08:01
 
| 08:01
|For example- to replace a base present at 5th position to alanine, type: '''dna3 within brackets 5 equal to within double quotes alphabet A.'''  Press '''Enter'''.
+
  Kum ka nuksa – ban bujli ia u base uba don ha ka jaka ba 5 sha ka alanine, type: '''dna3 within brackets 5 equal to within double quotes alphabet A.'''  Nion '''Enter'''.
(Nuksa  – ban weng/bujli ia u base uba don ha ka jaka ba 5 sha ka alanine, type: '''dna3 within brackets 5 equal to within double quotes alphabet A.'''  Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 08:19
 
| 08:19
|For the output, type: '''dna3'''. Press '''Enter'''.
+
  Na ka bynta ka output, type: '''dna3'''. Nion '''Enter'''.
(Na ka bynta ka output, type: '''dna3'''. Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 08:24
 
| 08:24
|Observe the output. The '''cytosine''' at position 5 is replaced with '''alanine'''.
+
  Khmih thuh ia ka output. Ka '''cytosine''' ha ka jaka ba 5 la shah bujli da u '''alanine'''.
(Ha khmih  ia ka output. Ka '''cytosine''' ha ka jaka ba 5 la shah bujli da u '''alanine'''.)
+
  
 
|-
 
|-
 
| 08:31
 
| 08:31
| To replace a part of the '''string''', type the following command.
+
  Ban bujli ia ka shi bynta jong u '''string''', type ia ka command ba harum.
(Ban weng  i bynta jong u '''string''', type ia ka command ba harum.)
+
  
 
|-
 
|-
 
| 08:35
 
| 08:35
|'''Dna3 within brackets 6 colon 10 equal to within double quotes ATGC.''' Press '''Enter'''.
+
  '''Dna3 within brackets 6 semi-colon 10 equal to within double quotes ATGC.''' Nion '''Enter'''.
('''Dna3 within brackets 6 colon 10 equal to within double quotes ATGC.''' Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 08:45
 
| 08:45
|For the output, type: '''dna3'''. Press '''Enter'''.
+
  Na ka bynta ka output, type: '''dna3'''. Nion '''Enter'''.
(Na ka bynta ka output, type: '''dna3'''. Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 08:52
 
| 08:52
|The output shows the 4 bases from the position  6 to 9 are replaced with new bases '''ATGC'''.
+
  Ka output ka pyni ia ki 4 tylli ki bases na ka jaka ba 6 haduh 9 kiba shah bujli da ki bases '''ATGC''' ba thymmai.  
(Ka output ka pyni ia ki 4 bases na ka jaka ba 6 haduh 9 kiba shah bujli da ki bases '''ATGC''' ba thymmai.)
+
  
 
|-
 
|-
 
| 09:01
 
| 09:01
| Once you have edited your sequence object, convert it back to the “read only” form.
+
  Shisien ba phi lahdep dep pynkylla ia ka sequence object, pynkylla biang ia ka sha ka “read only” form.
(Marsien  dep pynkylla ia ka sequence object, pynkylla biang ia ka sha ka “read only” form.)
+
  
 
|-
 
|-
 
| 09:07
 
| 09:07
|Type the following '''dna4 equal to dna3 dot to seq open and close parenthesis'''. Press '''Enter'''.
+
  Type kumne harum'''dna4 equal to dna3 dot to seq open and close parenthesis'''. Nion '''Enter'''.
(Type kumne harum'''dna4 equal to dna3 dot to seq open and close parenthesis'''. Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 09:19
 
| 09:19
|For the output, type: '''dna4.''' Press '''Enter'''.
+
  Na ka bynta ka output, type: '''dna4.''' Nion '''Enter'''.
(Na ka bynta ka output, type: '''dna4.''' Nion '''Enter'''.)
+
  
 
|-
 
|-
 
| 09:25
 
| 09:25
| Let's summarize.
+
  To ngin batai lyngkot
(To ngin ia khmih ia kiba ngi lah kdew haneng )
+
 
+
 
|-
 
|-
 
| 09:27
 
| 09:27
|In this tutorial, we have learnt to: *  Generate a random DNA sequence
+
  Ha kane ka tutorial, ngi lah pule ban *  Generate a random DNA sequence
(Ha kane ka jingbatai (tutorial) , ngi lah nang  ban *  Generate a random DNA sequence)
+
  
 
|-
 
|-
 
| 09:32
 
| 09:32
| Slice a DNA sequence at specified locations
+
  Slice ia ka DNA sequence ha ki jaka ba lah buh.
(Pynpra  ia ka DNA sequence ha ki jaka ba lah buh.)
+
  
 
|-
 
|-
 
| 09:36
 
| 09:36
| Join two sequences together to form a new sequence, that is, to concatenate.
+
  Pyndait lang ar tylli ki sequence ban ioh ia ka sequence ba thymmai, kata ka mut, ban pynlong kawei.
(Pyndait lang ar tylli ki sequence ban ioh ia ka sequence ba thymmai, kata ka mut, ban lum lang .)
+
  
 
|-
 
|-
 
| 09:43
 
| 09:43
| We have also learnt how to: * use '''len, count''' and '''find''' functions
+
  Ngi lah pule ruh kumno ban: * use '''len, count''' bad '''find''' functions.
(Ngi lah nang  ruh kumno ban: * use '''len, count''' bad '''find''' functions.)
+
  
  
 
|-
 
|-
 
| 09:49
 
| 09:49
| convert a sequence object to a mutable sequence object and replace a base or part of the string.
+
  Ban pynkylla ia ka sequence object sha ka mutable sequence object bad ban bujli ia u base lane shi bynta jong u string.
(Ban pynkylla ia ka sequence object sha ka mutable sequence object bad ban bujli ia u base lane bynta jong u string.)
+
  
 
|-
 
|-
 
| 09:57
 
| 09:57
|For the assignment, generate a random '''DNA sequence''' of 30 bases.
+
  Na ka bynta ka assignment, wad ia uno uno u '''DNA sequence''' uba 30 bases.
(Na ka bynta ka assignment, wad ia uno uno u '''DNA sequence''' uba 30 bases.)
+
  
 
|-
 
|-
 
| 10:02
 
| 10:02
|Using Biopython tools, calculate the GC percentage and molecular weight of the sequence.
+
  Da kaba pyndonkam da u Biopython tools, khein ia ka GC percentage bad molecular weight jong ka sequence.  
(Da kaba pyndonkam da u Biopython tools, khein ia ka GC percentage bad molecular weight jong ka sequence.)
+
  
 
|-
 
|-
 
| 10:09
 
| 10:09
|Your completed assignment will be as follows.
+
  Ka assignment ba lah dep jong phi kan long kumne harum.
(Ka assignment ba lah dep jong phi kan long kumne harum.
+
  
 
|-
 
|-
 
| 10:13
 
| 10:13
|The output shows the '''GC''' content as percentage.
+
  Ka output ka pyni ia ka '''GC'''content ha ka percentage.
(Ka output kan  pyni ia ka '''GC'''content ha ka percentage.)
+
  
 
|-
 
|-
 
| 10:18
 
| 10:18
| The output shows the molecular weight of the DNA sequence.
+
  Ka output ka pyni ia ka molecular weight jong ka DNA sequence.
(Ka output kan  pyni ia ka molecular weight jong ka DNA sequence.)
+
  
 
|-
 
|-
 
| 10:23
 
| 10:23
| 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.)
+
  
 
|-
 
|-
 
| 10:26
 
| 10:26
|If you do not have good bandwidth, you can download and watch it.
+
  Lada phim don ka bandwidth ba biang, phi lah ban download bad peit ia ka.
(Lada phim don ka bandwidth ba biang, phi lah ban download bad peit ia ka.)
+
  
 
|-
 
|-
 
| 10:30
 
| 10:30
| We conduct workshops and give certificates.
+
  Ngi pynlong workshops bad ai certificates.
(Ngi ju pynlong ia ki  workshops bad sam ruh ia ki  certificates.)
+
  
 
|-
 
|-
 
| 10:32
 
| 10:32
|Please contact us.
+
  Sngewbha thoh sha ngi
(Sngewbha pyntip ia  ngi)
+
  
 
|-
 
|-
 
| 10:35
 
| 10:35
| Spoken-Tutorial project is supported by the National Mission on Education through ICT, MHRD, Government of India.
+
  Ia ka Spoken-Tutorial project la kyrshan da ka National Mission on Education through ICT, MHRD, Government of India.
(Ia ka Spoken-Tutorial project la kyrshan da ka National Mission on Education through ICT, MHRD, Government of India.)
+
  
 
|-
 
|-
 
| 10:43
 
| 10:43
| This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.
+
  ïa kane ka script la pynkylla sha ka Ktien Khasi da u Yuwanki Yolande Kharlukhi na Shillong, Bad ma nga u Hezekiah Lyngdoh, ngan pynkut noh. Khublei ba phi la ïasnoh lang.
(Nga dei ka Snehalatha na '''IIT Bombay''', signing off. Khublei shibun )
+
 
|}
 
|}

Revision as of 20:40, 21 April 2018

Time Narration
00:01 Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka Manipulating Sequences.


00:06 Ha kane ka tutorial, ngin pyndonkam ki tools ka Biopython: Ban pynmih ia u random DNA sequence
00:13
  Phiah ia u DNA sequence ha ki jaka ba lah buh
00:17
  Pyndait lang ia artylli ki sequences ban pynlong kawei ka sequence ba thymmai
00:22
  Wad ia ka jingjrong jong ka sequence
00:26
   Niew ia ki number jong ki  base lane ki dkhot jong u string
00:31
  Wad ia u base ba la thmu lane bynta jong u string
00:35
  Pynkylla ia ka sequence object sha ka mutable sequence object
00:40
  Ban bud ia kane ka tutorial, phi dei ban tip bha ia ka undergraduate Biochemistry lane Bioinformatics
00:47
  Bad ka basic Python programming
00:51

Lada em, peit ia ki tutorials Python ha ka link ba la ai

00:56
  Ban record ia kane ka tutorial, nga pyndonkam da ka * Ubuntu OS version 14.10
01:03
  Python version 2.7.8
01:07
  Ipython interpreter version 2.3.0
01:12
  Biopython version 1.64.
01:16
  To ngin ia plie iaka terminal bad sdang ia ka ipython interpreter
01:21
  Nion lang ia u Ctrl, Alt and t key
01:26
  Ha ka prompt, type: "ipython" bad sa nion Enter
01:31
  Ka Ipython prompt kan sa mih ha ka screen
01:35
  Da kaba pyndonkam ia ka Biopython, ngi lah ban pynmih ia ka sequence object na ka bynta ka random DNA sequence ha kano kano ka jingjrong  
01:44
  To mynta ngin ia pynmih ia ka sequence object na ka bynta ka DNA sequence kaba 20 bases
01:50
  Ha ka prompt, type: "import random", bad nion Enter.
01:56
  Nangta, import Seq module na Bio package.
02:01
  Bunsien Seq ngi ju pronounce kum seek.
02:06
  Ha ka prompt, type: From Bio dot Seq import Seq. Nion Enter.
02:15
  Ngin pyndonkam da ka Bio.Alphabet module ban pyntikna ia ki alphabets ha ka DNA sequence
02:22
  Type: from Bio dot Alphabet import generic underscore dna. Nion Enter.
02:32
 Type ia ki command harum ban shna ia ka sequence object na ka bynta ka randon DNA sequence. 
02:38
  Buh ia ka sequence ha ka variable dna1
02:42
  Sngewbha peit: ha kane ka command, pyndonkam ar tylli ki single quotes ha ka jaka ka double quote. Nion Enter
02:50
  Na ka bynta ka output, type: dna1. Nion Enter
02:55
  Ka output ka pyni ia ka sequence object na ka bynta ka random DNA sequence. 
03:00
  Lada phi kwah ka sequence ba thymmai, nion u up-arrow key ban ioh ia ka juh ka command kum haneng. Nion Enter. 
03:11
  Na ka bynta ka output, type ia ka kyrteng ka variable dna1. Nion Enter
03:17
  Ka output ka pyni iaka DNA sequence ba thymmai kaba pher na kaba nyngkong.
03:23
  Shaphang ka Sequence Objects
03:25
  Ka sequence objects ha ka jingshisha ka long kum ka Python strings.
03:30
  Te, bud beit ia ka rukom leh kumba leh ia ka Python strings.
03:35
  Ha ka Python, ngi niew ia ki characters ha ka string kaba sdang na 0, ha jaka u 1.
03:41
  U character ba nyngkong ha ka sequence u dei u zero.
03:45
  Phai biang sha ka terminal.
03:47
  Teng teng ngi hap ban trei tang shi bynta jong ka sequence
03:52
  Mynta, ngin ia peit kumno ban sei ia ki bynta jong ka string bad buh ia ki kum ki sequence objects.
03:58
  Nuksa, ngin slice ia ka DNA sequence ha ki ar bynta.
04:04
 Nyngkong, hapdeng ki bases 6 bad 7.
04:08
  Kane kan sei ia ka fragment na kaba sdang jong ka sequence sha ka base ba 6 ha ka sequence.
04:15
  Ka slice ba ar kan dei hapdeng ka bases 11 bad 12.
04:20
  Ka fragment ba ar kan dei na ka base ba 12 shaduh ba kut jong ka sequence.
04:26
  Type ia ka command ba harum, ha ka prompt, ban sei ia ka fragment ba nyngkong. 
04:31
  String1 equal to dna1 within brackets 0 semi-colon 6.
04:39
  string1 ka dei ka variable ban lum ia ka fragment ba nyngkong.
04:43
  Ki command ba bud kin long beit kum ha ka Python.
04:47
 Hapoh kine ki brackets dei ki jaka ba sdang bad ba sangeh ba ba la pyniakhlad da u colon.
04:53
  Kine ki jaka ki kynthup lang ia kaba sdang hynrei khlem kynthup ïaki ha ka jaka ba sangeh. Nion Enter.
05:01
  Ban peit ia ka output, type: "string1", nion Enter.
05:04
 Ka output ka pyni ia ka fragment ba nyngkong kum ka sequence object.
05:10
  Ban sei ia ka string ba ar na ka sequence, nion ia u up-arrow key bad edit ia ka command kumne harum: 
05:17
  Pynkylla ia ka ka kyrteng jong u variable sha ka string2 bad jaka sha u 11 bad 20.  
05:24
  Na ka bynta ka output, type: "string2". Nion Enter.
05:30
  Mynta ngi ioh ia ka fragment ba ar ruh kum ka sequence object.
05:34
  To ngin pynlong ïaki kawei, kata, ban pyndait lang ia baroh ar ki strings  ban pynlong u fragment ba thymmai.
05:42
  Buh ia ka sequence ba thymmai ha ka variable dna2.
05:46
  Type: dna2 equal to string1 plus string2. Nion Enter.
05:53
  Sngewbha kynmaw ba: ngim lah ban thep ki sequence da ki alphabets ki bym iahap.
05:59
  Kata ka mut, ngim lah ban pynlong kawei ia ka DNA sequence bad ka protein sequence ban ioh ia ka sequence ba thymmai.
06:07
  Ki ar tylli ki sequences ki dei ban don kajuh ka alphabet attribute.
06:12
  Ban peit ia ka output, type: "dna2". Nion Enter.
06:17
  Ka output ka pyni ia ka sequence ba thymmai kaba dei ka jing pyndait lang jong u string1 bad string2.
06:23
  Ban ioh ia ka jingjrong jong ka sequence ba thymmai, ngin pyndonkam da ka len function. 
06:29
  Type: "len" hapoh parenthesis"dna2". Nion Enter.
06:34
  Ka output ka pyni ia ka sequence kaba jrong 15 bases.
06:39
 Ngi lah ruh ban niew ia ka jingdon jong ki bases bapher bapher ha ka sequence. 
06:44
  Ban leh ia kane, ngin pyndonkam da ka count   function.
06:47
  Kum ka nuksa – ban niew ia ka jingdon jong u alanines ba don ha ka sequence, ngi type ia ka command ka ba harum: dna2 dot count hapoh parenthesis hapoh double quotes alphabet A. 
07:02
  Nion Enter.
07:04
  Ka output ka pyni ia ka jingdon jong u alanines ha ka sequence dna2.
07:10
  Ban shem ia u jait base ne u dkhot jong u string, ngin pyndonkam da u find   function.
07:16
  Type: dna2 dot find hapoh parenthesis hapoh double quotes "GC". Nion Enter.
07:26
  Ka output ka pyni ia ka jaka ba nyngkong kaba mih ka GC ha u string.
07:32
  Ha ka jingshisha ia ka sequence object um ju lah ban pynkylla.
07:35
  Ban pynkylla ia ka sequence, ngi dei ban pynkylla iaka sha ka mutable sequence object.
07:41
  Ban leh ia kane, type: dna3 equal to dna2 dot to mutable plie bad khang ia u parenthesis. Nion Enter.
07:52
  Na ka bynta ka output, type: dna3 Nion Enter.
07:55
  Mynta ngin sa lah ban pynkylla ia ka sequence object.
07:59
  To ngin ia bujli ia u base na ka sequence.
08:01
  Kum ka nuksa – ban bujli ia u base uba don ha ka jaka ba 5 sha ka alanine, type: dna3 within brackets 5 equal to within double quotes alphabet A.  Nion Enter.
08:19
  Na ka bynta ka output, type: dna3. Nion Enter.
08:24
  Khmih thuh ia ka output. Ka cytosine ha ka jaka ba 5 la shah bujli da u alanine.
08:31
  Ban bujli ia ka shi bynta jong u string, type ia ka command ba harum.
08:35
  Dna3 within brackets 6 semi-colon 10 equal to within double quotes ATGC. Nion Enter.
08:45
  Na ka bynta ka output, type: dna3. Nion Enter.
08:52
  Ka output ka pyni ia ki 4 tylli ki bases na ka jaka ba 6 haduh 9 kiba shah bujli da ki bases ATGC ba thymmai. 
09:01
  Shisien ba phi lahdep dep pynkylla ia ka sequence object, pynkylla biang ia ka sha ka “read only” form.
09:07
  Type kumne harumdna4 equal to dna3 dot to seq open and close parenthesis. Nion Enter.
09:19
  Na ka bynta ka output, type: dna4. Nion Enter.
09:25
  To ngin batai lyngkot
09:27
  Ha kane ka tutorial, ngi lah pule ban *  Generate a random DNA sequence
09:32
  Slice ia ka DNA sequence ha ki jaka ba lah buh.
09:36
  Pyndait lang ar tylli ki sequence ban ioh ia ka sequence ba thymmai, kata ka mut, ban pynlong kawei.
09:43
  Ngi lah pule ruh kumno ban: * use len, count bad find functions.


09:49
  Ban pynkylla ia ka sequence object sha ka mutable sequence object bad ban bujli ia u base lane shi bynta jong u string.
09:57
  Na ka bynta ka assignment, wad ia uno uno u DNA sequence uba 30 bases.
10:02
  Da kaba pyndonkam da u Biopython tools, khein ia ka GC percentage bad molecular weight jong ka sequence. 
10:09
  Ka assignment ba lah dep jong phi kan long kumne harum.
10:13
  Ka output ka pyni ia ka GCcontent ha ka percentage.
10:18
  Ka output ka pyni ia ka molecular weight jong ka DNA sequence.
10:23
  Kane ka video ka batai lyngkot ia ka Spoken Tutorial project. 
10:26
  Lada phim don ka bandwidth ba biang, phi lah ban download bad peit ia ka.
10:30
  Ngi pynlong workshops bad ai certificates.
10:32
  Sngewbha thoh sha ngi
10:35
  Ia ka Spoken-Tutorial project la kyrshan da ka National Mission on Education through ICT, MHRD, Government of India.
10:43
  ïa kane ka script la pynkylla sha ka Ktien Khasi da u Yuwanki Yolande Kharlukhi na Shillong, Bad ma nga u Hezekiah Lyngdoh, ngan pynkut noh. Khublei ba phi la ïasnoh lang.	

Contributors and Content Editors

Hezekiah2016, PoojaMoolya