Biopython/C2/Writing-Sequence-Files/English - Revision history

PoojaMoolya at 10:04, 28 September 2015

2015-09-28T10:04:03Z

PoojaMoolya at 09:47, 28 September 2015

2015-09-28T09:47:20Z

Show changes

Snehalathak at 09:51, 24 September 2015

2015-09-24T09:51:44Z

Snehalathak at 06:47, 24 September 2015

2015-09-24T06:47:26Z

Snehalathak: Created page with " {| style="border-spacing:0;" ! Visual Cue ! Narration |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;..."

2015-09-24T06:43:23Z

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 #000001;..."

New page

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

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 1'''

'''Title Slide'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Hello everyone.

Welcome to this tutorial on '''Writing Sequence Files'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 2'''

'''Learning Objectives'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| In this tutorial, we will learn how to,

* Create Sequence Record Objects.
* Write sequences files.
* Convert between file formats.
* And sort records in a file by length.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 3'''

'''Pre-requisites'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| To follow this tutorial you should be familiar with,

* Undergraduate Biochemistry or Bioinformatics
* And basic Python programming

Refer to the Python tutorials at the given link.

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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 4'''

'''System Requirement'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right: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
* And Biopython 1.64

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 5'''

'''SeqIO functions'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| We have earlier learnt about

'''parse''' and '''read''' functions to read contents of a file.

In this tutorial we will learn how to use '''write''' function to write sequences to a file.

And use '''Convert''' function for interconversion between various file formats.

Let me now demonstrate how to use '''write''' function.

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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Navigate to the file, “example-insulin”.

Open text file “example-insulin” in a text editor.

Highlight sequence, GI accession number.

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Here is a text file with a protein sequence.

The sequence shown here is insulin protein.

The file also has information such as GI accession number and also description.

We will now create a file for this sequence in FASTA format.

The first step is to create sequence record object.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 6'''

'''Sequence Record Objects'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| More information about Sequence Record Objects:

It is the basic data type for the sequence input/output interface.

In sequence record object, a sequence is associated with higher level features:

such as identifiers and descriptions.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Press ctrl, alt ant t keys simultaneously on the keyboard.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Open the terminal by pressing ctrl, alt and t keys simultaneously .

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Type,

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

'''from Bio.SeqRecord import SeqRecord '''

'''from Bio.Alphabet import generic_protein'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| At the prompt type ipython, press enter.

At the prompt type the following lines:

From '''Bio dot Seq module''' import '''Seq class'''.

From '''Bio dot SeqRecord module''' import '''Sequence Record class'''

From B'''io dot Alphabet module''' import '''generic protein class'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''record1 = SeqRecord(Seq(“MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG” \'''

'''+ “GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN”, generic_protein),'''

'''id= “gi|386828|gb|AAA59172.1”,'''

'''description= “insulin [Homo sapiens]”)'''

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Next I will save the sequence record object in a variable '''record1.'''

Copy the sequence, id and description from the text file and paste in the respective lines on the terminal.

Press enter.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Type, '''record1'''.

Press enter'''.'''

Highlight the output.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| To view the output, type, '''record1'''.

Press enter.

The output shows the insulin protein sequence as sequence record object.

It shows the sequence along with id and description.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Type,

f'''rom Bio import SeqIO'''

'''SeqIO.write(record1, "example.fasta", "fasta")'''

Press enter
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| We will use write function to convert the above sequence object to a FASTA file.

Import SeqIO module from Bio package.

Next type the command line with a '''write''' function to convert the sequence object to FASTA file.

'''write '''function takes 3 arguments, first one is the variable storing the sequence record object.

Second is the file name to write the FASTA file.

The Third is the file format to write.''' '''

Press enter.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Highlight the output.

Cursor on the terminal.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Output shows “one”, that is we have converted one sequence record object to a FASTA file.

The file in FASTA format is saved in the home folder as '''"example.fasta".'''

Let me warn you:

The output will over-write any pre-existing file of the same name.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Navigate to the home folder and click on the file, “my_example.fasta”.

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| To view the file

Navigate to the file in the home folder.

Open this file in a text editor.

The protein sequence is now in FASTA format.

Close the text editor.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Cursor on the terminal.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Many bioinformatics tools take different input file formats.

So sometimes there is a need to interconvert between sequence file formats.

We can do file conversions using''' convert '''function in SeqIO module.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Navigate to home folder and click on “HIV.gb” .

Open HIV.gb using text editor.

Scroll down the page.

Close the text editor.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| For demonstration I will convert a GenBank file to a FASTA file.

I have a GenBank file in my home folder.

Let me open this in a text editor.

This file contains HIV genome in GenBank format.

This GenBank file has descriptions of all the genes in the genome in the first part of the file.

It is followed by a complete genome sequence.

Close the text editor.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Type the following lines on the terminal.

>>>'''from Bio import SeqIO '''

'''SeqIO.convert("HIV.gb", "genbank", "HIV.fasta", "fasta")'''

press enter

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Type the following lines on the terminal.

Here the '''convert''' function converts the complete genome sequence present in the GenBank file to FASTA file.

Press enter

The new file in FASTA format is now saved as HIV.fasta in the home folder.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Navigate to the file and open '''my_example-2.fasta.'''

Close the text editor.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Navigate to the file and open in the text editor.

Close the text editor.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 7'''

'''Limitations of convert function.'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Even though we can convert the file formats easily using '''convert''' function, it has limitations.

Writing some formats requires information which other file formats don’t contain.

For example: We can convert a GenBank file to a FASTA file, we can't do the reverse.

Similarly we can turn a FASTQ file into a FASTA file, but can’t do the reverse.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Cursor on the terminal.

Type

'''>>> from Bio import SeqIO '''

'''>>> help(SeqIO.convert)'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| For more information regarding convert function, type the help command.

Press enter.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Press “q” on the key board.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Press “'''q'''” on the key board to get back to the prompt.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Cursor on the terminal.

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| We can also extract individual genes from the HIV genome in GenBank format.

These individual genes can be saved in FASTA or any other formats.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Type the following at the prompt:

'''from Bio import SeqIO '''

'''f = open('HIV_gene.fasta', 'w') '''

'''for genome in SeqIO.parse('HIV.gb','genbank'): '''

'''for gene in genome.features: '''

'''if gene.type == "CDS": '''

'''gene_seq = gene.extract(genome.seq) '''

'''gi = str(gene.qualifiers['db_xref']).split(":")[1].split("'")[0] '''

'''f.write(">GeneId %s %s\n%s\n" % (gi, gene.qualifiers['product'], gene_seq)) '''

'''f.close() '''

'''Press enter '''

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| For this type the following code at the prompt.

This code will write all individual '''CDS''' gene sequences , their ids and name of the gene in a file.

This file is saved as “'''HIV_geneseq.fasta'''” on your home folder.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Navigate to home folder and open “hemoglobin.fasta”.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Using Biopython tools we can sort the records in a file by length.

Here I have opened a FASTA file “'''hemoglobin.fasta'''” which has six records.

Each record is of a different length.

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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| At the prompt type,

'''from Bio import SeqIO '''

'''records = list(SeqIO.parse("hemoglobin.fasta","fasta")) '''

'''records.sort(cmp=lambda x,y: cmp(len(y),len(x))) '''

'''SeqIO.write(records, "sorted_hemoglobin.fasta", "fasta")'''

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Type the following lines to arrange the longest record first.

The new file with the sorted sequences will be saved as''' "sorted_hemoglobin.fasta" '''in your home folder'''.'''

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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Cursor on the terminal.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| For Short records first, reverse the arguments in the records.sort command line.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 8'''

Summary
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Lets Summarize,

In this tutorial we have learnt to,

* Create Sequence Record Objects.

* Write sequence files using''' write''' function of Sequence Input/Output module( Bio.SeqIO.

* Convert between sequence file formats using '''convert''' function.

* And sort records in a file by length.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 9'''

'''Assignment'''

'''from Bio import SeqIO'''

'''record = SeqIO.read(“HIV.gb”, “genbank”)'''

'''record'''

'''sub_record = record [4587:5165] # GI = 19172951, ID 155459, “HIV1gp3”'''

'''SeqIO.write (sub_record, “sub_record-2.fasta”, “fasta”)'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| For Assignment:

Extract the gene "'''HIV1gp3'''" at positions 4587 to 5165 from the genomic sequence of HIV.

The file “'''HIV.gb'''” is included in code files of this tutorial.

Your completed assignment should have the following code.

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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 10'''

'''Acknowledgement '''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide Number 11'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.

For more details, please write to us.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide number 12'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this Mission is available at the link shown.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''Slide number 12'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

@@ Line 34: / Line 34: @@
-* Undergraduate Biochemistry or Bioinformatics
+* Undergraduate '''Biochemistry''' or '''Bioinformatics'''
-* And basic Python programming
+* And basic '''Python''' programming
-Refer to the Python tutorials at the given link.
+Refer to the '''Python''' tutorials at the given link.
 |-
@@ Line 45: / Line 45: @@
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| To record this tutorial I am using
-* Ubuntu OS version. 14.10
+* '''Ubuntu OS''' version. 14.10
-* Python version 2.7.8
+* '''Python''' version 2.7.8
-* Ipython interpretor version 2.3.0
+* '''Ipython interpretor''' version 2.3.0
-* And Biopython 1.64
+* And '''Biopython''' 1.64

@@ Line 9: / Line 9: @@
 '''Title Slide'''
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Hello everyone.
 Welcome to this tutorial on '''Writing Sequence Files'''.
@@ Line 135: / Line 136: @@
 |-
-| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| '''record1 = SeqRecord(Seq(“MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG” \'''
+| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:none;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| Type,
-'''+ “GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN”, generic_protein),'''
+'''QLENYCN”, generic_protein),'''
@@ Line 196: / Line 215: @@
-The Third is the file format to write.
+The Third is the file format to write.''' '''
@@ Line 209: / Line 228: @@
-The file in FASTA format is saved in the home folder as '''example.fasta.'''
+The file in FASTA format is saved in the home folder as '''"example.fasta".'''
@@ Line 456: / Line 475: @@
 | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000001;border-left:1pt solid #000001;border-right:1pt solid #000001;padding-top:0.097cm;padding-bottom:0.097cm;padding-left:0.062cm;padding-right:0.097cm;"| For Assignment:
-Extract the gene '''HIV1gp3''' at positions 4587 to 5165 from the genomic sequence of HIV.
+Extract the gene "'''HIV1gp3'''" at positions 4587 to 5165 from the genomic sequence of HIV.
-The file '''HIV.gb''' is included in code files of this tutorial.
+The file “'''HIV.gb'''” is included in code files of this tutorial.