H-Tuple Approach to Evaluate Statistical Significance of Biological Sequence Comparison with Gaps
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Afshin Fayyaz movaghar
We propose an approximate distribution for the gapped local score of a two sequence comparison. Our method stands on combining an adapted scoring scheme that includes the gaps and an approximate distribution of the ungapped local score of two independent sequences of i.i.d. random variables. The new scoring scheme is defined on h-tuples of the sequences, using the gapped global score. The influence of h and the accuracy of the p-value are numerically studied and compared with obtained p-value of BLAST. The numerical experiments emphasize that our approximate p-values outperform the BLAST ones, particularly for both simulated and real short sequences.
©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston
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- Normalization of Dye Bias in Microarray Data Using the Mixture of Splines Model
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- Using Duplicate Genotyped Data in Genetic Analyses: Testing Association and Estimating Error Rates
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- Super Learning: An Application to the Prediction of HIV-1 Drug Resistance
- Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo
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- Statistical Inference for Quantitative Polymerase Chain Reaction Using a Hidden Markov Model: A Bayesian Approach
- A Bayesian Model of AFLP Marker Evolution and Phylogenetic Inference
- Sequential Quantitative Trait Locus Mapping in Experimental Crosses
- Case-Control Inference of Interaction between Genetic and Nongenetic Risk Factors under Assumptions on Their Distribution
- Inference on the Limiting False Discovery Rate and the P-value Threshold Parameter Assuming Weak Dependence between Gene Expression Levels within Subject
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