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Basic Amino Acid Alignment Search Model Documents

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Main Document

Basic Amino Acid Alignment Search Model 

written by Tyler Murray

Basic Amino Acid Alignment Search Model evolves a DNA sequence and compares it to the original to estimate the probability of a genetic mutation by generating a matrix called a Point Accepted Mutation (PAM) matrix.  One PAM is the amount of time it takes for 1% of the amino acids to mutate and is estimated to be about 1 million years. The PAM matrix estimates the likelihood that an amino acid in row i will replace the amino acid in column j.  Raising PAM to the nth power results in a matrix that gives us the likelihood for replacements after n time units.

The Basic Amino Acid Alignment Search Model is distributed as a ready-to-run (compiled) Java archive.   Double clicking the jar file will run the program if Java is installed.  You can modify this simulation if you have EJS installed by right-clicking within the map and selecting "Open Ejs Model" from the pop-up menu item.

Published December 23, 2014
Last Modified January 1, 2015

This file has previous versions.

Supplemental Documents

Basic Local Alignment Search Tool Report 

Final project report for the Basic Local Alignment Search Tool.

Last Modified January 1, 2015

This file is included in the full-text index.

Source Code Documents

Basic Amino Acid Alignment Search Source Code 

The source code zip archive contains an XML representation of the Basic Amino Acid Alignment Search Model.  Unzip this archive in your EjsS workspace to compile and run this model using EjsS.

Last Modified January 1, 2015

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