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Trends in Bioinformatics
  Year: 2011 | Volume: 4 | Issue: 1 | Page No.: 10-22
DOI: 10.3923/tb.2011.10.22
 
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Evaluation of Prediction Accuracy of Genefinders Using Mouse Genomic DNA
J. Nasiri, A. Haghnazari and M. Alavi

Abstract:
Six gene-finding programs i.e., Genscan, GeneMark hmm., HMMgene, GenView2, FGENESH and FGENESH+ were evaluated using 24 well defined mouse single- and multiexon genes to predict the structure of protein coding genes. Our analyses indicated that different methods often produce different and sometimes contradictory-results. In the nucleotide level, the highest correlation coefficient (0.87) and approximate correlation (0.86) values and also the lowest correlation coefficient (0.67) and approximate correlation (0.67) values were detected only for FGENESH+ and GenView 2 programs, respectively. Furthermore, at the exon level, similar results were obtained. In general, our results at either the nucleotide or exon levels showed that FGENESH+ (HMM plus sequence similarity programs), provide a level of improvement over the ab initio gene prediction methods such as Genview 2 and suggested that, probably, FGENESH+ and also Genscan can be more helpful than the others. Meanwhile, based on phylogenetic tree, all ab initio genefinders, excepted of GeneMarkhmm., were placed in the same group and FGENESH+ with GeneMarkhmm. programs assigned in another one. Moreover, based on our results, we realized that the accuracy of these programs, is strongly dependent on GC content. At last, on the basis of whole known sequences it was concluded that predictive accuracy of these programs is lower than actual.
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How to cite this article:

J. Nasiri, A. Haghnazari and M. Alavi, 2011. Evaluation of Prediction Accuracy of Genefinders Using Mouse Genomic DNA. Trends in Bioinformatics, 4: 10-22.

DOI: 10.3923/tb.2011.10.22

URL: https://scialert.net/abstract/?doi=tb.2011.10.22

 
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