* Author: Wesley Carl Maness

* Email: wesley.maness@yale.edu

* Class: MBB452/CPSC752

* Assignment: Final Project

* Due: April 29, 2005

* By comparing the frequency of codons in a region of an species genome

* read in a given frame with the typical frequency of codons in the

* species genes, it is possible to estimate a likelihood of the

* region coding for a protein in such a frame. Regions in which codons

* are used with frequencies similar to the typical species codon

* frequencies are likely to code for genes (exons) while regions

* which codons distribution is uniform -- 1/64 (0.015625) -- could

* be considered as non-coding regions (introns).

*

* Algorithm: In my implementation I use the Table of Human Codon Frequencies

* which is a log likliehood scale. I use a size 120(configurable) window and slide this window

* throughout the entire DNA raw sequence and for each sequence compute its

* log likliehood value from the table. Then I scan the entire array of these values

* and identify sequences of positive values: sequences in which there are positive

* values are more likely to be those of coding region for the Homo Sapiens species.

* I simply scan until I find the first positive, then last positive and repeat and

* display those sequences that are positive.

*

* Reference: The Table of Human Codon Frequencies is from the Weismann Institute

* of Science.

 

NOTE: Due to particular browser policies (active content)  please use Microsoft's IE.  I am not condoning Microsoft, instead I am simply suggesting use of their browser due to its lack of security, making it easier for my Applet to work in-browser.  Firefox, however,  will cause problems and not run Coding Finder correctly.  If you get any errors please email me.  Thanks!

 

Code Package:  all files in one: {zip file}, {CodingRegionFinder.java}, {CodingRegionFinderApplet.java}, {DataLoader.java}, {freq.txt}, and a sample DNA sequence from Homo Sapiens dUTPase exon 3 {sequence}.