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Sequence Alignment Term Project

for

CHEM 434 – BIOINFORMATICS

Prof. Ja= mil Momand and Prof. Nancy Warter-Perez

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Due date= :  Tuesday, June 7th 1:30 – 4:00 p.m. (Final Exam Period)

 

If you successfully complete the base project, you will receive a B on your project.  = If you successfully complete both the base project and one extension, you will rec= eive an A on your project.  If you successfully complete one further extension you will receive a hundr= ed percent on your project.  Note: Presentation grades are separate (Overall grade: 90% project and 10% presentation).

 

Base project (Global alignment using dynamic programming):

Implement global alignment using dynamic programming (similar to Smith-Waterman’s algorithm).  Use PAM and BLOSSUM scoring matric= es and assume a fixed gap penalty (given by the matrix).

 

The program should prompt the user to enter the scoring matrix file name and two sequences.  The program should display the aligned sequences, showing gaps (-) in each sequence and the matches (|) between the sequences, and the alignment score.

 

 

Extensions (Select 1 of the following):=

= 1.      Extend your program to support local alignment algorithm (Smith-Waterman). 

= 2.      Extend your program to support affine gap penalties.  Use the gap penalty from the scori= ng matrix for your gap open penalty. &nb= sp;

= 3.      Modify your program to work with a query sequence and a database.  In this case, instead of prompting= the user for two sequences, the program should prompt the user for the query sequence and the database flat file.  The format of each entry in the database flat file is:=

> sequence identifying information

{sequence without spaces or= newline characters}

The program should also prompt the user for a = score threshold.  All sequences that exceed that score will be displayed (ideally in order from highest score to lowest score).  =

 

Project Presentation

 

Each group will give a 15-20 minute presentation follo= wed by a 10-minute question period.  = Each group member should participate in the presentation.  The presentation should include a = demonstration of your software and a discussion of the algorithms used. 

Suggestions for organization of presentations:

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