Biopython/C2/Blast/English-timed - Revision history

Sandhya.np14 at 15:48, 20 July 2018

2018-07-20T15:48:38Z

PoojaMoolya at 07:51, 10 March 2017

2017-03-10T07:51:09Z

Snehalathak at 06:50, 5 January 2017

2017-01-05T06:50:47Z

Snehalathak at 06:46, 5 January 2017

2017-01-05T06:46:51Z

Snehalathak at 05:51, 5 January 2017

2017-01-05T05:51:21Z

Sandhya.np14 at 12:12, 4 August 2016

2016-08-04T12:12:26Z

Sandhya.np14 at 08:23, 3 August 2016

2016-08-03T08:23:36Z

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PoojaMoolya: Created page with "{| Border=1 ! Time ! Narration |- | 00:01 | Welcome to this tutorial on''' BLAST''' using Biopython tools. |- | 00:06 | In this tutorial, w..."

2016-06-06T06:45:51Z

Created page with "{| Border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Welcome to this tutorial on''' BLAST''' using Biopython tools. |- | 00:06 | In this tutorial, w..."

New page

{| Border=1
! <center>Time</center>
! <center>Narration</center>

|-
| 00:01
| Welcome to this tutorial on''' BLAST''' using Biopython tools.

|-
| 00:06
| In this tutorial, we will learn: To run '''BLAST''' for the query sequence using Biopython tools

|-
|00:13
|And parse the '''BLAST''' output for further analysis.

|-
| 00:17
|To follow this tutorial you should be familiar with, Undergraduate '''Biochemistry''' or '''Bioinformatics'''

|-
|00:24
|And basic '''Python''' programming

|-
|00:27
|Refer to the '''Python''' tutorials at the given link.

|-
| 00:31
|To record this tutorial, I am using,'''Ubuntu''' Operating System version. 14.10

|-
|00:37
|'''Python''' version 2.7.8

|-
|00:41
| '''Ipython interpretor''' version 2.3.0

|-
|00:46
|'''Biopython''' version 1.64 and a working Internet connection

|-
| 00:52
|'''BLAST''' is the acronym for '''Basic Local Alignment Search Tool.'''

|-
|00:57
|It is an algorithm for comparing sequence information.

|-
| 01:02
|The program compares '''nucleotide''' or '''protein''' sequences to sequences in databases and calculates the statistical significance of matches.

|-
|01:14
| There are two different ways to run ''BLAST''':

|-
|01:17
|Local '''BLAST''' on your machine or Run '''BLAST''' over Internet through NCBI servers.

|-
| 01:24
|Running '''BLAST''' in '''Biopython''' has two steps.

|-
|01:28
|First, run '''BLAST''' for your query sequence and get some output.

|-
|01:33
|Second, parse the '''BLAST''' output for further analysis.

|-
| 01:38
|We will open the '''terminal''' and run '''BLAST''' for a nucleotide sequence.

|-
|01:43
|Open the terminal by pressing Ctrl, Alt and T keys simultaneously.

|-
| 01:48
|At the '''prompt''' type '''ipython''' and press '''Enter'''.

|-
| 01:52
|In this tutorial I will demonstrate how to run '''BLAST''' over internet using '''NCBI BLAST''' service.

|-
|02:01
|Type the following at the '''prompt''': Import '''NCBIWWW''' module from '''Bio.Blast''' package. Press '''Enter'''.

|-
| 02:14
|Next to run the '''BLAST''' over internet: type the following at the '''prompt'''

|-
|02:20
|We will use '''qblast function '''in the '''NCBIWWW '''module.

|-
| 02:25
|'''qblast function''' takes three '''arguments''':

|-
|02:29
|The first '''argument''' is the '''blast program''' to use for the search.

|-
|02:33
|Second specifies the databases to search against.

|-
|02:38
|The third '''argument''' is a your '''query sequence.'''

|-
| 02:43
| The input for the '''query sequence''' can be in the form of '''GI''' number or a '''FASTA''' file Or it can also be a '''sequence record object'''.

|-
| 02:53
| For this demonstration, I am using the '''GI number''' for a '''nucleotide sequence'''.

|-
|02:58
|The '''GI number''' is for a '''nucleotide sequence''' of '''insulin'''.

|-
| 03:03
|The '''qblast function''' also takes a number of other option '''arguments'''.

|-
|03:09
|These '''arguments''' are analogous to the different parameters you can set on the '''BLAST''' web page.

|-
|03:15
|The '''qblast function''' will return the '''BLAST''' results in '''xml''' format.

|-
| 03:20
|Back to the '''terminal'''.

|-
|03:22
|We have to use the appropriate '''Blast''' program,

|-
|03:25
|depending on whether our query sequence is a '''nucleotide''' or '''protein sequence'''.

|-
|03:30
|Since our query is a '''nucleotide''', we will use '''blastn '''program''' and '''nt''' refers to the '''nucleotide''' database.

|-
|03:39
|Details about this are available at the '''NCBI BLAST''' webpage.

|-
| 03:45
|The blast output is stored in the variable '''result''' in the form of an '''xml''' file.

|-
|03:51
|Press '''Enter'''.

|-
| 03:53
| Depending upon the speed of your Internet, it may take a few minutes to complete the '''BLAST''' search.

|-
| 03:59
| It is important to save the '''xml''' file on the disk before processing further.

|-
|04:05
|Type the following lines to save the '''xml file. '''

|-
|04:09
|These lines of code will save the search result as '''blast.xml''' in the home folder.

|-
| 04:18
| Navigate to your home folder and locate the file.

|-
|04:21
|Click on the file and check the contents of the file.

|-
| 04:30
| Use the code shown in this text file if you want to use a '''FASTA''' file as a query.

|-
| 04:36
| Here is the code if you want to use '''sequence record object''' from a '''FASTA''' file as a query.

|-
| 04:42
|Back to the '''terminal'''.

|-
|04:44
|The next step is to parse the file to extract data.

|-
|04:48
|The First step in parsing is to open the '''xml''' file for input.

|-
|04:53
|Type the following at the '''prompt'''. Press '''Enter'''.

|-
| 04:57
|Next import the module '''NCBIXML''' from '''Bio.Blast''' package.

|-
|05:05
|Press '''Enter'''.

|-
| 05:07
|Type the following lines to parse the Blast output.

|-
|05:11
|A '''BLAST''' record contains all the information you want to extract from the '''BLAST''' output.

|-
| 05:18
|Let us print out some information about all hits in our blast report greater than a particular threshold.

|-
|05:27
|Type the following code

|-
|05:30
|For a match to be significant, expect score should be less than 0.01.

|-
| 05:37
| For each '''hsp''' that is high scoring pair, we get the '''title''', '''length''','''hsp''' score '''gaps and '''expect value'''.

|-
|05:49
|We also print strings containing the '''query''' , the aligned database sequence and string specifying the match and mismatch positions

|-
|06:02
|Press '''Enter''' key twice to get output.

|-
| 06:05
| Observe the output:

|-
|06:09
|For each alignment we have '''length''', '''score''', '''gaps''', '''evalue''' and '''strings'''.

|-
| 06:16
|You can extract the required information using other '''functions''' available in '''Bio.Blast''' package.

|-
|06:24
|We have come to the end of this tutorial.

|-
| 06:26
| Let's summarize,

|-
|06:27
|In this tutorial we have learnt to Run '''BLAST''' for the query nucleotide sequence using '''GI''' number.

|-
|06:36
|And parse the '''BLAST''' output using '''Bio.Blast.Record''' module.

|-
| 06:43
| For the assignment, Run''' BLAST''' Search for a '''protein''' sequence of your choice.

|-
|06:50
|Save the output file and parse the data contained in the file.

|-
|06:55
|Your completed assignment should have the following lines of code, as shown in this file.

|-
|07:01
|Observe the code, Since our query is '''protein''' sequence, we have used '''blastp '''program and '''nr''' that is non-redundant '''protein''' database for the '''BLAST''' search.

|-
| 07:16
| The video at the following link summarizes the Spoken Tutorial project.

|-
|07:20
|Please download and watch it.

|-
| 07:22
| The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.

|-
|07:30
|For more details, please write to us.

|-
| 07:33
| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

|-
|07:40
|More information on this Mission is available at the link shown.

|-
| 07:45
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

@@ Line 9: / Line 9: @@
 |-
 | 00:06
-| In this tutorial, we will learn: * To '''run''' "BLAST" for the '''query sequence''' using Biopython tools
+| In this tutorial, we will learn: To '''run''' "BLAST" for the '''query sequence''' using Biopython tools
 |-

@@ Line 13: / Line 13: @@
 |-
 |00:13
-|* And, '''parse''' the BLAST output for further analysis.
+| And, '''parse''' the BLAST output for further analysis.
 |-
@@ Line 33: / Line 33: @@
 |-
 |00:37
-|* '''Python''' version 2.7.8
+| '''Python''' version 2.7.8
 |-
 |00:41
-|* '''Ipython interpretor''' version 2.3.0
+| '''Ipython interpretor''' version 2.3.0
 |-
 |00:46
-|* '''Biopython''' version 1.64 and * a working Internet connection.
+| '''Biopython''' version 1.64 and * a working Internet connection.
 |-
@@ Line 97: / Line 97: @@
 |-
 | 02:14
-|Next, to '''run''' the BLAST over internet, type the following at the prompt.
+|Next, to '''run''' the BLAST over internet, type the following at the prompt.result= NCBIWWW.qblast("blastn","nt","186429").
-−
 result= NCBIWWW.qblast("blastn","nt","186429").
 |-
@@ Line 279: / Line 277: @@
 |-
 | 06:26
-| Let's summarize.
+| Let's summarize.In this tutorial, we have learnt to run '''BLAST''' for the query nucleotide sequence using '''GI''' number.
-−
-|-
-|06:27
-|In this tutorial, we have learnt to run '''BLAST''' for the query nucleotide sequence using '''GI''' number.
 |-

@@ Line 93: / Line 93: @@
 |-
 |02:01
-|Type the following at the prompt: '''from Bio.Blast Import NCBIWWW'''.
+|Type the following at the prompt: '''from Bio.Blast Import NCBIWWW''' Press '''Enter'''.
-−
-Import '''NCBIWWW module''' from '''Bio.Blast package'''. Press '''Enter'''.
 |-

@@ Line 93: / Line 93: @@
 |-
 |02:01
-|Type the following at the prompt: '''Import NCBIWWW module from Bio.Blast''' package. Press '''Enter'''.
+|Type the following at the prompt: '''from Bio.Blast Import NCBIWWW'''.
 |-
 | 02:14
 |Next, to '''run''' the BLAST over internet, type the following at the prompt.
 |-

@@ Line 93: / Line 93: @@
 |-
 |02:01
-|Type the following at the prompt: '''Import NCBIWWW''' module from '''Bio.Blast''' package. Press '''Enter'''.
+|Type the following at the prompt: '''Import NCBIWWW module from Bio.Blast''' package. Press '''Enter'''.
 |-

@@ Line 9: / Line 9: @@
 |-
 | 00:06
-| In this tutorial, we will learn: * To '''run''' '''BLAST''' for the '''query sequence''' using Biopython tools
+| In this tutorial, we will learn: * To '''run''' "BLAST" for the '''query sequence''' using Biopython tools
 |-
 |00:13
-|* And, '''parse''' the '''BLAST''' output for further analysis.
+|* And, '''parse''' the BLAST output for further analysis.
 |-
@@ Line 157: / Line 157: @@
 |-
 |03:30
-|Since our query is a '''nucleotide''', we will use '''blastn '''program'''  and "nt" refers to the '''nucleotide''' database.
+|Since our query is a '''nucleotide''', we will use '''blastn '''program and "nt" refers to the '''nucleotide''' database.
 |-
@@ Line 201: / Line 201: @@
 |-
 | 04:36
-| Here is the code if you want to use '''sequence record object''' from a '''FASTA''' file as a query.
+| Here is the code, if you want to use '''sequence record object''' from a '''FASTA''' file as a query.
 |-
@@ Line 229: / Line 229: @@
 |-
 | 05:07
-|Type the following lines to parse the Blast output.
+|Type the following lines to '''parse''' the '''Blast''' output.
 |-
 |05:11
-|A BLAST '''record''' contains all the information you want to extract from the '''BLAST''' output.
+|A BLAST '''record''' contains all the information you want to '''extract''' from the '''BLAST''' output.
 |-
 | 05:18
-|Let us print out some information about all '''hit'''s in our '''blast report''' greater than a particular threshold.
+|Let us print out some information about all the '''hit'''s in our '''blast report''' greater than a particular threshold.
 |-
@@ Line 245: / Line 245: @@
 |-
 |05:30
-|For a match to be significant, expect score should be less than 0.01.
+|For a '''match''' to be significant, expect '''score''' should be less than 0.01.
 |-
 | 05:37
-| For each '''hsp''', that is, high scoring pair, we get the '''title''', '''length''','''hsp score, gaps''' and '''expect value'''.
+| For each '''hsp''', that is, high scoring pair, we get the '''title, length, hsp score, gaps''' and '''expect value'''.
 |-
 |05:49
-|We also print '''string'''s containing the '''query''' , the aligned database sequence and string specifying the match and mismatch positions.
+|We will also print '''string'''s containing the '''query''', the aligned database sequence and string specifying the match and mismatch positions.
 |-
 |06:02
-|Press '''Enter''' key twice to get output.
+|Press '''Enter''' key twice to get the output.
 |-
 | 06:05
-| Observe the output:
+| Observe the output.
 |-
@@ Line 269: / Line 269: @@
 |-
 | 06:16
-|You can extract the required information using other '''functions''' available in '''Bio.Blast''' package.
+|You can extract the required information using other '''functions''', available in '''Bio.Blast''' package.
 |-
@@ Line 281: / Line 281: @@
 |-
 |06:27
-|In this tutorial, we have learnt to run '''BLAST''' for the query nucleotide sequence, using '''GI''' number.
+|In this tutorial, we have learnt to run '''BLAST''' for the query nucleotide sequence using '''GI''' number.
 |-
@@ Line 301: / Line 301: @@
 |-
 |07:01
-|Observe the code. Since our query is '''protein''' sequence, we have used '''blastp '''program and '''nr''', that is, non-redundant '''protein''' database for the '''BLAST''' search.
+|Observe the code. Since our '''query''' is '''protein''' sequence, we have used '''blastp '''program and "nr", that is, non-redundant protein database for the '''BLAST''' search.
 |-