, Volume 22, Issue 1, pp 49-69
Date: 08 Feb 2007

Using a VOM model for reconstructing potential coding regions in EST sequences

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Abstract

This paper presents a method for annotating coding and noncoding DNA regions by using variable order Markov (VOM) models. A main advantage in using VOM models is that their order may vary for different sequences, depending on the sequences’ statistics. As a result, VOM models are more flexible with respect to model parameterization and can be trained on relatively short sequences and on low-quality datasets, such as expressed sequence tags (ESTs). The paper presents a modified VOM model for detecting and correcting insertion and deletion sequencing errors that are commonly found in ESTs. In a series of experiments the proposed method is found to be robust to random errors in these sequences.