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SequenceIt!

Allen Place and Tom Schmidt (Center of Marine Biotechnology, University of Maryland Biotechnology Institute)
Screen Shots | System Requirements

SequenceIt! is a simulation program that allows you to experience the art and logic of protein sequencing through experimentation. You are given a polypeptide or protein whose sequence (the linear arrangement of amino acids) and length are unknown. Your objective is to deduce the sequence of this polypeptide using many of the tools available to a practicing protein chemist.

You specify the operations and the order of their application. Success in determining the protein sequence depends on your understanding of the experimental procedures and on the logic you use in executing those procedures. Operations available range from simple cleavage reactions (enzymatic and chemical) which break a polypeptide into smaller fragments to complex sequential analyses (e.g., Edman degradation) that provide sequence information.

Screen Shots

A Problem Summary window showing treatment by performic acid oxidation and staphylococcal protease.

A SequenceIt! problem begins with an Eppendorf tube containing a certain amount of an unknown linear or circular polypeptide.

Within this window you are able to choose a variety of ways to view what you have done to the original polypeptide and what type of data or information is available on a specified object.

SequenceIt! replicates laboratory situations (with errors and ambiguities) and places limits on the amount of material available for study. You can set up SequenceIt! so as to use only a simple short polypeptide initially, and add new complexity as your grasp of protein chemistry grows. We have incorporated many organizational tools to help in hypothesis generation and data retrieval.

For instance, a summary of information for each peptide can be displayed in the Peptide Information window.

Peptide Information window displaying Edman Degradation results for a peptide fragment resulting from staphylococcal protease treatment of the original peptide.

 

System Requirements

Macintosh or Power Macintosh

  • System 6.07 or later; System 7.1 or later for Power Macintosh.
  • At least 1MB of available RAM, more for complex simulations.

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