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

Title Slide

Learning Objectives

• Run BLAST for the query sequence using Biopython tools

• And parse the BLAST output for further analysis.

Pre-requisites

• Undergraduate Biochemistry or Bioinformatics
• And basic Python programming

Refer to the Python tutorials at the given link.

System Requirement

• Ubuntu OS version. 14.10
• Python version 2.7.8
• Ipython interpretor version 2.3.0
• Biopython version 1.64
• And a working Internet connection

About BLAST

It is an algorithm for comparing sequence information.

About BLAST

• compares nucleotide or protein sequences to sequences in databases
• and calculates the statistical significance of matches.

About BLAST

• Local BLAST on your machine.

• Run BLAST over Internet through NCBI servers.

About BLAST

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.

Type, ipython and press enter.

>>> from Bio.Blast import NCBIWWW

Press enter.

Type the following at the prompt:

Import NCBIWWW module from Bio.Blast package.

Press Enter.

>>> result = NCBIWWW.qblast("blastn", "nt", "186429")

Type the following at the prompt,

We will use qblast function in the NCBIWWW module.

Highlight the arguments.

>>> result = NCBIWWW.qblast("blastn", "nt", "186429")

The first argument is the blast program to use for the search.

Second specifies the databases to search against.

The third argument is a your query sequence.

Or it can also be a sequence record object.

The GI number is for a nucleotide sequence of insulin.

qblast function.

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

The qblast function will return the BLAST results in xml format.

We have to use the appropriate Blast program,

depending on whether our query is a nucleotide or protein sequence.

Since our query is a nucleotide, we will use blastn program.

And nt refers to the nucleotide database.

NCBI BLAST website

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Press Enter.

>>> save_file = open("blast.xml", "w")

>>> save_file.write(result.read())

>>> save_file.close()

>>> result.close()

Press enter

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.

Click on the file and check the contents of the file.

from Bio.Blast import NCBIWWW

fasta_string = open("insulin.fasta").read()

result = NCBIWWW.qblast("blastn", "nt", fasta_string)

save_file = open("blast.xml", "w")

save_file.write(result.read())

save_file.close()

result.close()

result= open("blast.xml")

from Bio.Blast import NCBIWWW

from Bio import SeqIO

record = SeqIO.read("insulin.fasta", format="fasta")

result = NCBIWWW.qblast("blastn", "nt", record.seq)

save_file = open("blast.xml", "w")

save_file.write(result.read())

save_file.close()

result.close()

result= open("blast.xml")

>>>result = open("my_blast.xml")

press Enter.

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

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

Type the following at the prompt:

Press Enter.

press enter.

Press Enter.

>>>records = NCBIXM.parse(result)

>>>blast_record = records.next()

press enter

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

Type the following

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

for alignment in blast_record.alignments:

for hsp in alignment.hsps:

if hsp.expect <0.01:

print('****Alignment****')

print('sequence:', alignment.title)

print('length:', alignment.length)

print('score:', hsp.score)

print('gaps:', hsp.gaps)

print('e value:', hsp.expect)

print(hsp.query[0:90] + '...')

print(hsp.match[0:90] + '...')

print(hsp.sbjct[0:90] + '…')

Press Enter key twice.

We also print strings containing the query (query), the aligned database sequence (sbjct) and string specifying the match and mismatch positions (match).

Press Enter key twice to get output.

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

We have come to the end of this tutorial.

Summary

In this tutorial we have learnt to,

• Run BLAST for the query nucleotide sequence using GI number.

• And parse the BLAST output file using Bio.Blast.Record module.

Assignment

(use blastp)

result = NCBIWWW.qblast("blastp", "nr", 386828)

non-redundant protein database (nr).

Run BLAST

Search for a protein sequence of your choice.

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

Your completed assignment should have the following lines of code :

As shown in this text file.

Since our query is protein sequence, here we have used blastp program.

And nr non-redundant protein database for the BLAST search.

Acknowledgement

Please download and watch it.

For more details, please write to us.

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