PoojaMoolya at 06:06, 21 June 2018

2018-06-21T06:06:20Z

Hezekiah2016 at 05:56, 29 May 2018

2018-05-29T05:56:19Z

Hezekiah2016 at 05:54, 29 May 2018

2018-05-29T05:54:21Z

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Hezekiah2016 at 15:10, 21 April 2018

2018-04-21T15:10:02Z

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Hezekiah2016: 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..."

2018-02-02T12:14:52Z

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..."

New page

{| Border=1
|'''Time'''
|'''Narration'''

|-
| 00:01
| Welcome to this tutorial on '''Manipulating Sequences.'''
(Ngi pdiang sngewbha ia phi sha kane ka tutorial jong ka '''Manipulating Sequences.''')

|-
| 00:06
| 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
| Slice a DNA sequence at specified locations
(Phiah ia u DNA sequence ha ki jaka ba lah bynshet )

|-
| 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)

|-
| 00:22
| Find the length of the sequence
(Wad ia ka jingjrong jong ka sequence)

|-
| 00:26
| Count the number of individual '''base'''s or part of the '''string'''
( Niew ia ki number jong ki '''base''' s lane ki dkhot jong u '''string''')

|-
| 00:31
| Find a particular base or part of the string.
(Wad ia u base uba bniah lane bynta jong u string)

|-
| 00:35
| Convert a '''sequence object''' to a mutable sequence object.
(Pynkylla ia ka '''sequence object''' sha ka mutable sequence object)

|-
| 00:40
| To follow this tutorial, you should be familiar with undergraduate Biochemistry or Bioinformatics
(Ban sngewthuh ia kane ka tutorial, phi dei ban long kiba shemphang ha ka undergraduate Biochemistry lane Bioinformatics)

|-
| 00:47
|and basic Python programming.
(Bad ka basic Python programming)

|-
| 00:51
|If not, refer to the '''Python''' tutorials at the given link.
(lem kumta, pyndonkam da ka nuksa '''Python''' ha ka link ba bud )

|-
| 00:56
| To record this tutorial, I am using: * '''Ubuntu OS''' version 14.10
(Ban record ia kane ka nuksa , nga pyndonkam da ka * '''Ubuntu OS''' version 14.10)

|-
| 01:03
| '''Python''' version 2.7.8
('''Python''' version 2.7.8)

|-
| 01:07
| '''Ipython interpreter''' version 2.3.0
('''Ipython interpreter''' version 2.3.0)

|-
| 01:12
|'''Biopython''' version 1.64.
('''Biopython''' version 1.64.)

|-
| 01:16
|Let me open the '''terminal''' and start '''ipython interpreter'''.
(To ngin ia plie iaka '''terminal''' bad sdang ia ka '''ipython interpreter''')

|-
| 01:21
|Press '''Ctrl, Alt''' and '''t''' keys simultaneously.
(Nion sah ia u '''Ctrl, Alt''' and '''t''' key)

|-
|01:26
|At the prompt, type: "ipython" and press '''Enter'''.
(Ha ka prompt, type: "ipython" bad sa nion '''Enter''')

|-
| 01:31
|'''Ipython''' prompt appears on the screen.
(Ka '''Ipython''' prompt kan sa mih ha ka screen)

|-
| 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)

|-
| 01:44
|Let us now generate a sequence object for a DNA sequence of 20 bases.
(To ngin ia pynmih ia ka sequence object na ka bynta ka DNA sequence kaba 20 bases)

|-
|01:50
|At the prompt, type: "import random", press '''Enter'''.
(Ha ka prompt, type: "import random", bad nion '''Enter'''.)

|-
| 01:56
| Next, import '''Seq '''module from '''Bio '''package.
(Nangta, import '''Seq '''module na '''Bio '''package.)

|-
| 02:01
|Often '''Seq''' is pronounced as '''seek'''.
(Barabor '''Seq''' ngi shait ong '''seek'''.)

|-
| 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'''.)

|-
| 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)

|-
| 02:22
| Type: '''from Bio dot Alphabet import generic underscore dna.''' Press '''Enter'''.
(Type: '''from Bio dot Alphabet import generic underscore dna.''' Nion '''Enter'''.)

|-
| 02:32
| Type the following '''command''' to create a sequence object for the random DNA sequence.
(Type kumne harum '''command''' ban shna ia ka sequence object na ka bynta ka DNA sequence. )

|-
| 02:38
|Store the sequence in a variable '''dna1'''.
(Pynlang ia ka sequence ha ka variable '''dna1''')

|-
| 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''')

|-
| 02:50
| For the output, type: '''dna1'''. Press '''Enter'''.
(Na ka bynta ka output, type: '''dna1'''. Nion '''Enter''')

|-
| 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. )

|-
| 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'''.)

|-
| 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''')

|-
| 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.)

|-
| 03:23
| About '''Sequence Objects''':
(Shaphang ka '''Sequence Objects''')

|-
| 03:25
|The '''sequence objects''' usually act like normal '''Python string'''s.
(Ka '''sequence objects''' ha ka jingshisha ka long beit '''Python string'''s.)

|-
| 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.)

|-
| 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.)

|-
| 03:41
|The first character in the sequence is position zero.
(U character ba nyngkong ha ka sequence u dei u zero.)

|-
| 03:45
| Back to the terminal.
(Phai biang sha ka terminal.)

|-
| 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)

|-
| 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 dkhot jong ka string bad buh ia ki kum ki sequence objects.)

|-
| 03:58
|For example, we will '''slice''' the DNA sequence at two positions.
(Nuksa, ngin '''slice''' ia ka DNA sequence ha ki ar bynta.)

|-
| 04:04
|First, between bases 6 and 7.
(Nyngkong, hapdeng ki bases 6 bad 7.)

|-
| 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.)

|-
| 04:15
| The second slice will be between bases 11 and 12.
(Ka slice ba ar kan dei hapdeng ka bases 11 bad 12.)

|-
| 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.)

|-
| 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.)

|-
| 04:31
|'''String1 equal to dna1 within brackets 0 colon 6.'''
('''String1 equal to dna1 within brackets 0 colon 6.''')

|-
| 04:39
|'''string1''' is the variable to store the first fragment.
('''string1''' ka dei ka variable ban lum ia ka fragment ba nyngkong.)

|-
| 04:43
|The rest of the command follows as in normal Python.
(Ki command ba bud kin long beit kum ha ka Python.)

|-
| 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 kut ba shah phiah da u colon.)

|-
| 04:53
|The positions are inclusive of the start but exclusive of the stop position. Press '''Enter'''.
(Kine ki jaka (positions) ki lum lang ha kaba sdang hynrei kim shah lum shuh ha kaba kut . Nion '''Enter'''.)

|-
| 05:01
| To view the output, type: "string1", press '''Enter'''.
(Ban peit ia ka output, type: "string1", nion '''Enter'''.)

|-
| 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.)

|-
| 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: )

|-
| 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'''.)

|-
| 05:24
| For the output, type: "string2". Press '''Enter'''.
(Na ka bynta ka output, type: "string2". Nion '''Enter'''.)

|-
| 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.)

|-
| 05:34
| Let us concatenate, that is, add the two '''strings '''together to form a new fragment.
(To ngin ia lum lang , kata, ban pyndait lang ia baroh ar ki '''strings ''' ban ioh u fragment ba thymmai.)

|-
| 05:42
|Store the new sequence in a variable '''dna2'''.
(Buh ia ka sequence ba thymmai ha ka variable '''dna2'''.)

|-
| 05:46
|Type: '''dna2 equal to string1 plus string2'''. Press '''Enter'''.
(Type: '''dna2 equal to string1 plus string2'''. Nion '''Enter'''.)

|-
| 05:53
|Please note: we cannot add sequences with incompatible alphabets.
(Sngewbha tip ba : ngim lah ban iasnoh ia ki sequence bad ki alphabets ki bym iahap.)

|-
| 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 lum ia ka DNA sequence bad ka protein sequence ban ioh ia ka sequence ba thymmai.)

|-
| 06:07
|The two sequences must have the same alphabet attribute.
(Ki ar tylli ki sequences ki dei ban don kajuh ka alphabet attribute.)

|-
| 06:12
| To view the output, type: "dna2". Press '''Enter'''.
(Ban peit ia ka output, type: "dna2". Nion '''Enter'''.)

|-
| 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 jinglum kyllum jong u '''string1''' bad '''string2.''')

|-
| 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.)

|-
| 06:29
| Type: "len" within parenthesis "dna2". Press '''Enter'''.
(Type: "len" hapoh parenthesis"dna2". Nion '''Enter'''.)

|-
| 06:34
|Output shows the sequence as 15 bases long.
(Ka output ka pyni ia ka sequence kaba jrong 15 bases.)

|-
| 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.)

|-
| 06:44
|To do so, we will use '''count()''' function.
(Ban leh ia kane, ngin pyndonkam da ka '''count()''' function.)

|-
| 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.
(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
|Press '''Enter'''.
(Nion '''Enter'''.)

|-
| 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'''.)

|-
| 07:10
| To find a particular base or part of the string, we will use '''find()''' function.
(Ban wad ia u jait base ne u dkhot jong u string, ngin pyndonkam da u '''find()''' function.)

|-
| 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'''.)
|-
| 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.)

|-
| 07:32
| Normally a sequence object cannot be edited.
(Ha ka jingshisha ia ka sequence object um ju lah ban pynkylla.)

|-
| 07:35
|To edit a sequence, we have to convert it to the mutable sequence object.
(Ban pynkylla ia ka sequence, ngi hap ban pynkylla sha ka mutable sequence object.)

|-
| 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'''.)

|-
| 07:52
| For the output, type: '''dna3'''. Press '''Enter'''.
(Na ka bynta ka output, type: '''dna3''' Nion '''Enter'''.)

|-
| 07:55
| Now the sequence object can be edited.
(Mynta ngin sa lah ban pynkylla ia ka sequence object.)

|-
| 07:59
|Let us replace a '''base''' from the sequence.
(To ngin ia weng/bujli ia u '''base''' na ka sequence.)

|-
| 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'''.
(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
|For the output, type: '''dna3'''. Press '''Enter'''.
(Na ka bynta ka output, type: '''dna3'''. Nion '''Enter'''.)

|-
| 08:24
|Observe the output. The '''cytosine''' at position 5 is replaced with '''alanine'''.
(Ha khmih ia ka output. Ka '''cytosine''' ha ka jaka ba 5 la shah bujli da u '''alanine'''.)

|-
| 08:31
| To replace a part of the '''string''', type the following command.
(Ban weng i bynta jong u '''string''', type ia ka command ba harum.)

|-
| 08:35
|'''Dna3 within brackets 6 colon 10 equal to within double quotes ATGC.''' Press '''Enter'''.
('''Dna3 within brackets 6 colon 10 equal to within double quotes ATGC.''' Nion '''Enter'''.)

|-
| 08:45
|For the output, type: '''dna3'''. Press '''Enter'''.
(Na ka bynta ka output, type: '''dna3'''. Nion '''Enter'''.)

|-
| 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 bases na ka jaka ba 6 haduh 9 kiba shah bujli da ki bases '''ATGC''' ba thymmai.)

|-
| 09:01
| Once you have edited your sequence object, convert it back to the “read only” form.
(Marsien dep pynkylla ia ka sequence object, pynkylla biang ia ka sha ka “read only” form.)

|-
| 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'''.)

|-
| 09:19
|For the output, type: '''dna4.''' Press '''Enter'''.
(Na ka bynta ka output, type: '''dna4.''' Nion '''Enter'''.)

|-
| 09:25
| Let's summarize.
(To ngin ia khmih ia kiba ngi lah kdew haneng )

|-
| 09:27
|In this tutorial, we have learnt to: * Generate a random DNA sequence
(Ha kane ka jingbatai (tutorial) , ngi lah nang ban * Generate a random DNA sequence)

|-
| 09:32
| Slice a DNA sequence at specified locations
(Pynpra ia ka DNA sequence ha ki jaka ba lah buh.)

|-
| 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 lum lang .)

|-
| 09:43
| We have also learnt how to: * use '''len, count''' and '''find''' functions
(Ngi lah nang ruh kumno ban: * use '''len, count''' bad '''find''' functions.)

|-
| 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 bynta jong u string.)

|-
| 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.)

|-
| 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.)

|-
| 10:09
|Your completed assignment will be as follows.
(Ka assignment ba lah dep jong phi kan long kumne harum.

|-
| 10:13
|The output shows the '''GC''' content as percentage.
(Ka output kan pyni ia ka '''GC'''content ha ka percentage.)

|-
| 10:18
| The output shows the molecular weight of the DNA sequence.
(Ka output kan pyni ia ka molecular weight jong ka DNA sequence.)

|-
| 10:23
| This video summarizes the Spoken Tutorial project.
(Kane ka video ka lum kyllum ia ka Spoken Tutorial project.)

|-
| 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.)

|-
| 10:30
| We conduct workshops and give certificates.
(Ngi ju pynlong ia ki workshops bad sam ruh ia ki certificates.)

|-
| 10:32
|Please contact us.
(Sngewbha pyntip ia ngi)

|-
| 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.)

|-
| 10:43
| This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.
(Nga dei ka Snehalatha na '''IIT Bombay''', signing off. Khublei shibun )
|}

@@ Line 362: / Line 362: @@
 |-
 | 08:35
-| '''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'''.
 |-

@@ Line 4: / Line 4: @@
 | '''Narration'''
 |-
 | 00:01
 | Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka '''Manipulating Sequences.'''
 |-
@@ Line 28: / Line 26: @@
 |-
 | 00:26
-    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'''
 |-
@@ Line 152: / Line 150: @@
 |-
 | 03:25
-   Ka '''sequence objects''' ha ka jingshisha ka long kum ka '''Python string'''s.
+| Ka '''sequence objects''' ha ka jingshisha ka long kum ka '''Python string'''s.
 |-
@@ Line 405: / Line 403: @@
 | 09:43
 | Ngi lah pule ruh kumno ban: * use '''len, count''' bad '''find''' functions.
 |-

Biopython/C2/Manipulating-Sequences/Khasi - Revision history

PoojaMoolya at 06:06, 21 June 2018

Hezekiah2016 at 05:56, 29 May 2018

Hezekiah2016 at 05:54, 29 May 2018

Hezekiah2016 at 15:10, 21 April 2018

Hezekiah2016: 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..."