SIGRS
Class SIGRSScanForCCR

java.lang.Object
  SIGRS.SIGRSScanForCCR

public class SIGRSScanForCCR
extends java.lang.Object

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process. Significance of segments is evaluated using Karlin-Altschul statistics and specifically an extension by Karlin-Dembo allowing for nucleotides to have a Markov-dependence (see e.g. Karlin & Altschul (1993) and Karlin & Dembo (1992)

The routines are provided as is and no guarantee regarding stability etc. is given so use at your own risk!

See publication Larsson, P., Hinas, A., Ardell, D.H., Kirsebom, L.A., Virtanen, A. and Söderbom, F. De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring

Questions and comments can be directed to Pontus.Larsson@icm.uu.se

Constructor Summary

SIGRSScanForCCR(SIGRSScoreObject sso)

Method Summary

double[][]	findCCRs(int direction) Scores an input sequence and identifies contrasting composition regions (CCRs)
int	getModel()
int	getN()
java.lang.String[]	getSeqId()
int[]	getSeqLength()
void	setAlpha(double alpha)
void	setExpect(double expect)
void	setInFile(java.io.File[] inFile)
void	setModel(int model)
void	setN(int N)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SIGRSScanForCCR

public SIGRSScanForCCR(SIGRSScoreObject sso)

Method Detail

setN

public void setN(int N)

setModel

public void setModel(int model)

setExpect

public void setExpect(double expect)

setAlpha

public void setAlpha(double alpha)

setInFile

public void setInFile(java.io.File[] inFile)
               throws java.lang.Exception

Throws:

java.lang.Exception

getN

public int getN()

getSeqId

public java.lang.String[] getSeqId()

getSeqLength

public int[] getSeqLength()

getModel

public int getModel()

findCCRs

public double[][] findCCRs(int direction)
                    throws java.lang.Exception

Scores an input sequence and identifies contrasting composition regions (CCRs)

Parameters:

direction - The direction that is searched. The input sequence is always searched in the forward direction, this is to get the annotations correct. 1 -> forward strand, -1 -> reverse strand

Returns:

A matrix with CCRs where each row is a CCR and the columns are [0] -> start index (inclusive), [1] -> end index (exclusive), [2] -> orientation, [3] -> expect

Throws:

java.lang.Exception