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Bioinformatics Advance Access published online on October 25, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl544
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received May 18, 2006
Revised October 18, 2006
Accepted October 18, 2006

Article

Hypothesis testing approaches to the exon prediction problem

Mireia Vilardell 1 and Alex Sánchez-Pla 2 *

1 Statistics Department, University of Barcelona, Barcelona, Spain; Genetics Unit, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
2 Statistics Department, University of Barcelona, Barcelona, Spain

* To whom correspondence should be addressed.
Alex Sánchez-Pla, E-mail: asanchez{at}ub.edu


  Abstract

Motivation: Many gene identification methods assign scores to gene elements prior to their assembly into predicted genes. The scoring system is often based on log-likelihood ratios. These methods usually perform well but it is difficult to interpret how significant a score is.

Results: We have developed several tests of significance for the scores: (i) a Sum-of-Scores test (SST), (ii) an Intersection-Union test (IUT), based on a multiple hypothesis testing interpretation of an exon's score and (iii) a Meta-analytical approach (MA) which combines several p-values, corresponding to the exon's parts, to yield a global p-value.

We performed simulation studies which show that the Meta-Analytical approach has better sensitivity and specificity than other methods and is easier to interpret by non-expert users. This is an improvement over other methods and is especially relevant for users who would like to predict incomplete gene sequences.

Associate Editor: Dmitrij Frishman
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