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2015-07-23T11:55:15Z

Created page with " {| style="border-spacing:0;" ! <center>Visual Cue</center> ! <center>Narration</center> |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."

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{| style="border-spacing:0;"
! <center>Visual Cue</center>
! <center>Narration</center>

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''

'''Title Slide'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this tutorial on '''Manipulating Sequences.'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 2'''

'''Learning Objectives'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will use Biopython tools to;

1. Generate a random DNA sequence .

2. Slice a DNA sequence at specified locations.

3. Join two sequences together to form a new

sequence that is to Concatenate.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 3'''

'''Learning Objectives (Biopython Functions)'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 4. Find the length of the sequence.

5. Count the number of individual bases or part of the string.

6. Find a particular base or part of the string.

7. Convert a sequence object to a mutable sequence object.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 4'''

'''Pre-requisites'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should be familiar with,

Undergraduate Biochemistry or Bioinformatics

And Basic Python programming

If not:

Refer to the Python tutorials at the given link.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 5'''

'''System Requirement'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial I am using,

Ubuntu OS version. 14.10

Python version 2.7.8

Ipython interpretor version 2.3.0

Biopython version 1.64

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press ctrl, alt and t simultaneously.

At the prompt, type ipython.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let me open the terminal and start ipython interpretor.

Press ctrl, alt and t keys simultaneously.

At the prompt, type ipython and press enter.

Ipython prompt appears on the screen.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Generating random DNA sequence in python

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Using Biopython we can generate a sequence object for a random DNA sequence of any specified length.

Let us now generate a sequence object for a DNA sequence of 20 bases.

At the prompt. Type

'''import random'''

Press enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Fr At the prompt type

from Bio.Seq import Seq
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Next import '''Seq '''module from '''Bio '''package.

Often '''Seq''' is pronounced as '''seek'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''from Bio.Seq import Seq '''

Press Enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| At the prompt type,

'''From Bio dot Seq import Seq'''

'''(from Bio.Seq import Seq )'''

Press Enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We will use '''Bio.Alphabet''' module to specify the alphabets in the DNA sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''>>>from Bio.Alphabet import generic_dna'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Type,

'''from Bio dot alphabet import generic underscore dna.'''

'''(from Bio.Alphabet import generic_dna)'''

Press enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''dna1 = Seq( ''.join(random.choice('AGTC') for _ in range(30)),generic_dna) '''

Press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Type the following command to create a sequence object for the random DNA sequence;

Store the sequence in a variable '''dna1'''

Please note in this command use two single quotes instead of a double quote.

Press enter.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| type

>>>''' dna1'''

Press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For the output, type '''dna1.'''

Press enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Highlight output.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The output shows the sequence object for the random DNA sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.

Press up arrow key

Press enter.

type

>>>''' dna1'''

Press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| If you want a new sequence, press up arrow key to get the same command as above.

Press enter.

For the output, type the variable name, '''dna1.'''

Press enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The output shows a new DNA sequence, which is different from the first one.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 6and 7'''

'''Sequence Objects'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| About '''Sequence Objects'''

The '''sequence objects''' usually act like normal Python strings.

So follow the normal conventions as you do for Python strings

In Python,We count the characters in the string starting from 0 instead of 1.

The first character in the sequence is position zero.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.

At the prompt type,

'''string1 = my_seq[0:6] '''

Highlight the first string from 1-5th character.

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Back to the terminal.

Often you many need to work with only a part of the sequence.

Now lets see how to extract parts of the string and store them as sequence objects.

For example we will slice the DNA sequence at two positions.

First between bases 6 and 7.

This will extract a fragment from the beginning of the sequence to the 6th base in the sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Highlight the second string from 18th -30th character.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The second slice will be between bases 11 and 12.

The second fragment will be from the 12th base to the end of the sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| At the prompt type,

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Type the following command at the prompt to extract the first fragment.

'''String1 equal to dna1 within brackets 0 semicolon 6.'''

'''(string1 = dna1[0:6] )'''

'''string1''' is the variable to store the first fragment.

The rest of the command follows as in normal Python.

Enclosed in these brackets are the start and stop positions separated by a colon.

The positions are '''inclusive''' of the start, but '''exclusive''' of the stop position.

Press Enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''string1'''

press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To view the output

Type, '''string1,'''press enter.

The output shows the first fragment as the sequence object.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type

'''string2 = my_seq[11:20]'''

'''press enter'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To extract the second string from the sequence,

Press up arrow key and edit the command as follows:

Change the name of the variable to '''string2''', and positions to '''11 '''and '''20'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type '''string2'''

press enter.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For the output

Type

'''string2'''

press enter.

Now we have the 2nd fragment also as a sequence object.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type

'''dna2 = string1 + string2'''

press enter

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let us concatenate, that is, add the two '''strings '''together to form a new fragment:

Store the new sequence in a variable '''dna2'''.

Type,

'''dna2 equal to string1 plus string2'''

'''(dna2 = string1 + string2)'''

press enter

Please note;

we can not add sequences with incompatible alphabets.

That is we can not concatenate a DNA sequence and a protein sequence, to form a new sequence.

The two sequences must have the same alphabet attribute.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type

'''dna2'''

Press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To view the output, type '''dna2.'''

Press enter

The output shows a new sequence which is a combination of '''string1''' and '''string2.'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To find the length of the new sequence, we will use '''len '''function.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type

'''len(dna2)''' press Enter

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Type

'''len within parenthesis dna2.'''

'''(len(dna2))'''

press Enter

Output shows the sequence as 15 bases long.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''my_seq.count("A")'''

Press enter

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also count the number of individual bases present in the sequence.

To do so we will use '''count''' function.

For example to count the number of alanines present in the sequence .

Type the following command.

'''dna2 dot count within parenthesis within doublequotes alphabet A.'''

'''(dna2.count("A"))'''

press enter

The output shows the number of alanines present in the sequence '''dna2'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type

'''dna1.find(“AT”)'''

Press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To find a particular base or part of the string we will use '''find''' function.

Type

'''dna2 dot find within parenthesis within doublequotes GC.'''

'''dna2.find("GC")'''

press enter

The output indicates the position of the first instance of the appearance of '''GC''' in the string.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the terminal.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Normally a sequence object cannot be edited.

To edit a sequence we have to convert it to the mutable sequence object.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''dna3<nowiki>=</nowiki>dna2.tomutable()'''

press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To do so, type,

'''dna3 equal to dna2 dot tomutable open and close parenthesis.'''

'''(dna3<nowiki>=</nowiki>dna2.tomutable())'''

press enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type

'''dna3'''

press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For the output, type

'''dna3'''

press enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type

>>>'''mutable_seq[5]''A'''''

Press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now the sequence object can be edited.

Let us replace a base from the sequence.

For example to replace a base present at 5th position to alanine, type

'''dna3 within brackets 5 equal to within double quotes alphabet A.'''

'''(dna3[5]=''A'')'''

Press enter

For the output type '''dna3''' press enter.

Observe the output, the '''cytosine''' at position 5 is replaced with '''alanine'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''dna3[6:10]=''ATGC'''''

press enter

Highlight the output.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To replace a part of the string,

type the following command.

'''Dna3 within brackets 6 semicolon 10 equal to within double quotes ATGC'''

'''(dna3[6:10]=''ATGC'')'''

press enter

For the output type '''dna3''' press enter.

The output shows the 4 bases from position the 6 to 9 are replaced with new bases '''''ATGC'''''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''dna4<nowiki>=mutable_seq.toseq()</nowiki>'''

For the output type,

'''dna4'''

Press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Once you have edited your sequence object, convert it back to the '''“read only'''” form.

Type the following

'''dna4 equal to dna3 dot toseq open and close parenthesis.'''

'''(dna4<nowiki>=</nowiki>dna3.toseq())'''

Press enter.

For the output type '''dna4.'''

Press enter

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 8'''

Summary
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let's summarize,

In this tutorial, we have learnt to,

1. Generate a random DNA sequence.

2. Slice a DNA sequence at specified locations

3. Join two sequences together to form a new

sequence that is to Concatenate.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 9'''

'''Summary'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 4. We have also learnt how to use

len, count and find functions.

5. Convert a sequence object to a mutable sequence

object.

6. And replace a base or part of the string.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 10'''

Assignment

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For the assignment

* Generate a random DNA sequence of 30 bases. 

* Using Biopython tools calculate the GC percentage and Molecular Weight of the sequence. 

* Your completed assignment will be as follows.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| GC content of the DNA sequence.

Type,

'''from Bio.SeqUtils import GC'''

Press enter

Type

'''GC(dna)'''

Press enter

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The out put shows the GC content as percentage.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type,

'''from Bio.SeqUtils import molecular_weight'''

press enter

Then type,

'''molecular_weight(dna)'''

press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The output shows the molecular weight of the DNA sequence.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 11'''

'''Acknowledgement '''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This video summarizes the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 12'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We Conduct workshops and give certificates.

Please contact us.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 13'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Spoken-Tutorial project is supported by the National Mission on Education through ICT, MHRD, Government of India

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 13'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

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

Snehalathak: Created page with " {| style="border-spacing:0;" ! Visual Cue ! Narration |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."