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.
Please note that this resource requires
at least version 1.7 of Java (JRE).
Basic Local Alignment Search Tool Report
Final project report for the Basic Local Alignment Search Tool. download 900kb .pdf
Last Modified: January 1, 2015
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. download 1938kb .zip
Last Modified: January 1, 2015
T. Murray, Computer Program BASIC AMINO ACID ALIGNMENT SEARCH MODEL (2014), WWW Document, (https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13396&DocID=3981).
T. Murray, Computer Program BASIC AMINO ACID ALIGNMENT SEARCH MODEL (2014), <https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13396&DocID=3981>.
Murray, T. (2014). Basic Amino Acid Alignment Search Model [Computer software]. Retrieved May 27, 2023, from https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13396&DocID=3981
%0 Computer Program %A Murray, Tyler %D December 23, 2014 %T Basic Amino Acid Alignment Search Model %8 December 23, 2014 %U https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13396&DocID=3981
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The Easy Java Simulations Modeling and Authoring Tool is needed to explore the computational model used in the Basic Amino Acid Alignment Search Model.