Scenario: Comparison of genomes

BNFO 601

Fall 2010

Comparison of genomes to look for genes responsible for pathogenesis

Scientific story (html)

In brief: You hit on the idea of undestanding the basis for pathogenesis by the deadly E. coli O157:H7 by comparing its total complement of protein with that of the nonpathogenic strain E. coli K12. Unfortunately, the comparison nets you a file bigger than anything you could go through in a year. How can you extract the useful information from the file and put it in a form a human could understand?

Bioinformatic tools

Blast
Standard program to find similarities between sequences or sets of sequences.
Parsing program
Scans output, looking for items of interest as you define them. Outputs them to a separate file.

Perl focus: Pattern matching and extraction of strings through regular expressions
Suggested Reading: Beginning Perl (Simon Cozens), chapter 5, pp.147-162 (or if you like, 147-165)

Notes and papers

Molecular biology (PDF) (Questions)

Perna, N. T., G. Plunkett, 3rd, et al. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409(6819): 529-33.

Hayashi, T., K. Makino, et al. (2001). Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12." DNA Res 8: 11-22.

Blast/Parsing program (html) (Questions)
Regular expressions (html) (Questions)

Programs

Blast (obtainable from NCBI site - see instructions on how to download Blast, set up a database, and run the program)
Most people run this program off of the web. The point of interest for now is learning how to download the program so that you can tailor it to your own purposes.
Protein databases (obtainable from TIGR-CMR site - see instructions on how to download and which set to download).
Files containing all proteins deduced from completed DNA sequences of E. coli strains, used by Blast.

Parsing program:

BlastParser.pl- takes output from Blast, extracts information

BlastParserNative.pl - same as above, but more as a Perl programmer would write it

71vsnps.txt - data program was designed to handle

EdVsK12s.txt - Small portion of expected output from BlastAll

Additional programs:

matchtest.pl - Allows quick tests of regular expressions

HTML_to_text.pl - Sample program using regular expressions

Problem Set - Molecular biology (PDF)
Problem Set - Programming (html)

Presentation powerpoint - Sept. 8, 2006 (ppt)

Blast output:

edl_out.txt - Blast K12 vs. EDL output, e value 0.00001
sakai_out.txt - Blast K12 vs. Sakai output, e value 0.00001