Search results for "L-tuples"
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Alignment Free Dissimilarities for Nucleosome Classification
2016
Epigenetic mechanisms such as nucleosome positioning, histone modifications and DNA methylation play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have shown a role of DNA sequences in recruitment of epigenetic regulators. For this reason, the use of more suitable similarities or dissimilarity between DNA sequences could help in the context of epigenetic studies. In particular, alignment-free dissimilarities have already been successfully applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles…
Alignment free Dissimilarities for sequence classification
2015
One way to represent a DNA sequence is to break it down into substrings of length L, called L-tuples, and count the occurence of each L-tuple in the sequence. This representation defines a mapping of a sequence into a numerical space by a numerical feature vector of fixed length, that allows to measure sequence similarity in an alignment free way simply using disssimilarity functions between vectors. This work presents a benchmark study of 4 alignment free disssimilarity functions between sequences, computed on their L-tuples representation, for the purpose of sequence classification. In our experiments, we have tested the classes of geometric-based, correlation-based and information-based …