Difference between revisions of "Biopython/C2/Blast/English-timed"

| Welcome to this tutorial on''' BLAST''' using Biopython tools.

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

|And parse the '''BLAST''' output for further analysis.

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

|And basic '''Python''' programming  

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

|'''Python''' version 2.7.8

|'''Biopython''' version 1.64 and a working Internet connection

|It is an algorithm for comparing sequence information.

| There are two different ways to run ''BLAST''':

|Local '''BLAST''' on your machine or Run '''BLAST''' over Internet through NCBI servers.

|First, run '''BLAST''' for your query sequence and get some output.  

|Second, parse the '''BLAST''' output for further analysis.

|Open the terminal by pressing Ctrl, Alt and T keys simultaneously.  

|At the '''prompt''' type '''ipython''' and press '''Enter'''.

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

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

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

|Second specifies the databases to search against.

|The third '''argument''' is a your '''query sequence.'''

| 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'''.

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

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

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

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

|Type the following lines to save the '''xml file. '''

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

| Navigate to your home folder and locate the file.

| Use the code shown in this text file if you want to use 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.  

|The next step is to parse the file to extract data.

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

|Type the following at the '''prompt'''. Press '''Enter'''.

|Next import the module '''NCBIXML''' from '''Bio.Blast''' package.

|Type the following lines to parse the Blast output.

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

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

|Type the following code  

|For a match to be significant, expect score should be less than 0.01.

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

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

|Press '''Enter''' key twice to get output.

| Observe the output:

|For each alignment we have '''length''', '''score''', '''gaps''', '''evalue''' and '''strings'''.

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

| Let's summarize,

 

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

|And parse the '''BLAST''' output using '''Bio.Blast.Record''' module.

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

|Save the output file and parse the data contained in the file.

|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.

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

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

| This is Snehalatha from IIT Bombay signing off. Thank you for joining.