We present a modification to Phred and a program to detect heterogeneous positions in phred/phrap genome assemblies. This is particularly useful in the identification of mutation, co-existence or any other interesting sites in the assembly.

 

 

 
 
Program Details
Files to Download

This is our modified version of Phred. Installation is the same as the original Phred. Our version of Phred will give the same output files as the original Phred, except in addition, it will store peak values for each position in a directory called "trace_dir".

This is our program, DetectHetero, that is able to find all positions that possess heterogeneity properties. It can only be used on our modified version of Phred.

Experiment Results

The Severe Acute Respiratory Syndrome (SARS) presented us with a unique opportunity for our program to display its usage. A total of 17 SARS-CoV strains were assembled in GIS. We applied our modified version of Phred to trace files of all 17 SARS-CoV strains and assembled them using Phrap. DetectHetero was then applied to all 17 assemblies. A summary of the results can be found in the Word document below.