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Remote Blast

In this assignment, you will use BioPython to run a Blast job at NCBI.

Data

Download the human CST3 protein sequence.

Preliminaries

Figure out what Blast does and how it works.
Go to the NCBI Blast web page (find it yourself...) and start a Blast comparison with CST3 against the so-called non-redundant protein database: nr. This means that you comparison should use the "blastp" subprogram (protein query against protein DB).
Find the highest scoring hit in mouse
1. What is the E-value, and what does that mean?
2. Look at the actual alignment. How alike are the sequences?

Programming

Write a Python program that conducts a Blast search of a given protein sequence against the nr database at NCBI. There is good support for this in BioPython.

Requirements

Your program is an executable Python file taking one input: a file containing a protein sequence.
Output is the blast report given in XML format, presented to stdout.

To present:

You should be able to give a brief explanation of Blast.
What is the E-value, and what does that mean?
You should understand the online output from a Blast run.
Your code for the remoteblast program.
Demonstrate a successful run of remoteblast.

Example session

Usage of your program should be something like this:

orange-01> ./remoteblast cst3.fa
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>blastx</BlastOutput_program>
  <BlastOutput_version>blastx 2.2.6 [Apr-09-2003]</BlastOutput_version>
  <BlastOutput_reference>~Reference: Altschul, Stephen F., et al (1997), "Gapped 
BLAST and PSI-BLAST: a new generation of protein database search~programs",  
Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
  <BlastOutput_db>sprot</BlastOutput_db>
  <BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
  <BlastOutput_query-def>CST3</BlastOutput_query-def>
...

Output trimmed for brevity! Note that "orange-01>" is the commandline prompt.