Java Applet for Endspace Free Alignment

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Java Applet for End-space Free Alignment

• Xinwei Li

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Outline

• Background Introduction
• End-space Free Alignment
• Program Demonstration
• Software Structure
• Conclusion

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Background Introduction

• The Sequence Assembly Problem
• One has a set of partially overlapping
  subsequences that come from many copies of one
  original but unknown DNA sequence. The problem
  is to use comparisons of pairs of subsequences to
  infer the original sequence.
• A T C G G C T A A
• C G G A C T A C T
• A A T C C G A G C T T C T

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End-space Free Alignment

• Definition
• Given two sequences s and t, find the prefix of
  one having the maximal global alignment with a
  suffix of the other.

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Dynamic Programming

• Suppose sm, tp.
• Base
• dw(0s0, 0 t j) dw(0si, 0 t 0)0
• Recursion dw(0si, 0 t j) max
• dw(0s(i-1), 0 t (j-1)) w(si, tj),
• dw(0s(i-1), 0 t j) w(si, -),
• dw(0si, 0 t (j-1)w(-,tj ))

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Retrace the Alignment

• Search for j such as dw(0sm, 0 t j)
  max1lt j lt p (dw(0sm, 0 t j)) (bottom row)
• Search for i such as dw(0si, 0 t p)
  max1lt i lt m (dw(0si, 0 t p)) (right most
  column)
• The alignment score d max(dw(0sm, 0 t j),
  dw(0si, 0 t p))
• One retraces the alignment going left and up till
  it meets a 0 in the left most column or in the
  top row.

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Program Demonstration

• System Requirement
• A java applet supported browser with JRE version
  1.1 or later.
• Visit the EndFreeApplet.html in the package.
• http//www.cs.yorku.ca/xwli/
• classes\EndFreeApplet.html

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Software Structure
Applet Window
User Interface
Alignment Algorithm
Dialog Window
List View
Matrix View
Tool Bar
Data Storage
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Data Flow
Input
Output
Output
Applet Window
List View
Matrix View
Alignment Algorithm
Dialog Window
Data Storage
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Class Relationship
Algorithm
User Interface
Storage
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Data Storage

• Matrix -- contains a series of CellCollection
  objects.
• CellCollection -- represents a row in the matrix.
• UnitCell -- represents a cell in the matrix.

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Alignment Algorithm

• Alignment -- an abstract class that defines the
  basic data fields and methods for alignment.
• EndAlignment -- a subclass of class Alignment
  that implements the details about end-space free
  alignment.

Future implementation
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Algorithm Flow Chart
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User Interface

• EndFreeApplet
• parameters input window
• ListItemRender and MatrixView
• results ouput window
• DialogResult
• control center to connect the data storage
  objects with the views and receive commands from
  user

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Conclusion

• In this project, a Java applet with GUI is
  designed and implemented to perform the End-space
  Free Alignment according to the general alphabet
  for nucleotides and amino acids.
• The whole framework is designed to be extensible
  so that new alignment algorithm can be easily
  incorporated into it.

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Thank You

• Q A