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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.

Please note that this resource requires at least version 1.7 of Java (JRE).
1 supplemental document is available
1 source code document is available
Subjects Levels Resource Types
Modern Physics
- Biophysics
- Medical Physics
- Upper Undergraduate
- Graduate/Professional
- Instructional Material
= Simulation
Intended Users Formats Ratings
- Learners
- Researchers
- Educators
- application/java
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Access Rights:
Free access
License:
This material is released under a GNU General Public License Version 3 license.
Rights Holder:
Tyler Murray
Record Cloner:
Metadata instance created January 1, 2015 by Wolfgang Christian
Record Updated:
January 1, 2015 by Wolfgang Christian
Last Update
when Cataloged:
December 23, 2014
ComPADRE is beta testing Citation Styles!

Record Link
AIP Format
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).
AJP/PRST-PER
T. Murray, Computer Program BASIC AMINO ACID ALIGNMENT SEARCH MODEL (2014), <https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13396&DocID=3981>.
APA Format
Murray, T. (2014). Basic Amino Acid Alignment Search Model [Computer software]. Retrieved December 18, 2017, from https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13396&DocID=3981
Chicago Format
Murray, Tyler. "Basic Amino Acid Alignment Search Model." https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13396&DocID=3981 (accessed 18 December 2017).
MLA Format
Murray, Tyler. Basic Amino Acid Alignment Search Model. Computer software. 2014. Java (JRE) 1.7. 18 Dec. 2017 <https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13396&DocID=3981>.
BibTeX Export Format
@misc{ Author = "Tyler Murray", Title = {Basic Amino Acid Alignment Search Model}, Month = {December}, Year = {2014} }
Refer Export Format

%A Tyler Murray
%T Basic Amino Acid Alignment Search Model
%D December 23, 2014
%U https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13396&DocID=3981
%O application/java

EndNote Export Format

%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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Basic Amino Acid Alignment Search Model:

Is Based On Easy Java Simulations Modeling and Authoring Tool

The Easy Java Simulations Modeling and Authoring Tool is needed to explore the computational model used in the Basic Amino Acid Alignment Search Model.

relation by Wolfgang Christian

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