Title :
The influence of the background model on DNA motif prediction: An assessment for zinc finger transcription factor ZFX
Author :
Lihu, Andrei ; Holban, Stefan
Author_Institution :
Dept. of Comput. Sci., Politeh. Univ. of Timisoara, Timisoara, Romania
Abstract :
Motif finding is a computationally expensive procedure subject to noise and false positives, but of major importance in understanding gene expression and cancer. Several authors argued in favor of using higher order background models to better discriminate motifs. This paper studies the effect of using Markov higher order models in three commonly used algorithms to identify the ZFX transcription factor´s binding sites from a mouse embryonic stem cells dataset. We conclude that there are particular Markov orders that yield improved outcomes for each algorithm.
Keywords :
DNA; Markov processes; biology computing; cancer; DNA motif prediction; Markov higher order models; ZFX transcription factor; expensive procedure subject; gene cancer; gene expression; motif finding; mouse embryonic stem cells dataset; procedure subject; zinc finger transcription factor ZFX; Algorithm design and analysis; Bioinformatics; Computational modeling; DNA; Markov processes; Predictive models; Stem cells;
Conference_Titel :
Applied Computational Intelligence and Informatics (SACI), 2015 IEEE 10th Jubilee International Symposium on
Conference_Location :
Timisoara
DOI :
10.1109/SACI.2015.7208216