Class EvaluateGenePredictions

Object

EvaluateGenePredictions

public class EvaluateGenePredictions
extends Object

The EvaluateGenePredictions class takes a file of gene predictions output by the HMM application and compares it to a file of documented genes to determine how well the predictions match up with the documented genes - the program reports the sensitivity and specificity of the gene predictions.

Constructor Summary

Constructors

Constructor and Description
EvaluateGenePredictions()

Method Summary

Methods

Modifier and Type	Method and Description
static void	comparePredictedAnnotationToDocumentedGenes(String gene_fileName, String annotation_fileName) Compares gene predictions (as output by a HMM) with documented genes in a genome.
static void	main(String[] args) The main method takes two files, a file containing information about documented genes and a file containing gene predictions output by a HMM, and it compares the two, reporting the sensitivity and specificity of the gene predictions.

Methods inherited from class Object

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

Constructor Detail

EvaluateGenePredictions

public EvaluateGenePredictions()

Method Detail

comparePredictedAnnotationToDocumentedGenes

public static void comparePredictedAnnotationToDocumentedGenes(String gene_fileName,
                                               String annotation_fileName)

Compares gene predictions (as output by a HMM) with documented genes in a genome. The sensitivity and specificity of the gene predictions are output to the screen. The sensitivity of gene predictions is reported both on the forward strand of a genomic sequence (for HMMs that only predict genes on a single strand) and on both strands of a genomic sequence (for HMMs that predict genes on either strand). The sensitivity is the percent of documented coding nucleotides that are correctly predicted as coding nucleotides. The specificity is the percent of documented non-coding (i.e., intergenic) nucleotides that are correctly predicted as non-coding nucleotides.

Parameters:

gene_fileName - the name of a file containing information about documented genes

annotation_fileName - the name of a file output by a HMM containing gene predictions

main

public static void main(String[] args)

The main method takes two files, a file containing information about documented genes and a file containing gene predictions output by a HMM, and it compares the two, reporting the sensitivity and specificity of the gene predictions.

Parameters:

args - an array of Strings representing any command line arguments