T. Kjosmoen and T. Ryen and T. Eftestøl
Exploring the Combinatorics of Motif Alignments Foraccurately Computing Evalues from Pvalues
906 - 912
2009
3
4
International Journal of Computer and Information Engineering
https://publications.waset.org/pdf/9120
https://publications.waset.org/vol/28
World Academy of Science, Engineering and Technology
In biological and biomedical research motif finding tools are important in locating regulatory elements in DNA sequences. There are many such motif finding tools available, which often yield position weight matrices and significance indicators. These indicators, pvalues and Evalues, describe the likelihood that a motif alignment is generated by the background process, and the expected number of occurrences of the motif in the data set, respectively. The various tools often estimate these indicators differently, making them not directly comparable. One approach for comparing motifs from different tools, is computing the Evalue as the product of the pvalue and the number of possible alignments in the data set. In this paper we explore the combinatorics of the motif alignment models OOPS, ZOOPS, and ANR, and propose a generic algorithm for computing the number of possible combinations accurately. We also show that using the wrong alignment model can give Evalues that significantly diverge from their true values.
Open Science Index 28, 2009