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In this paper, we discuss an efficient and effective index mechanism to support the matching of massive pattern strings in against a very long target string. It is very important to the next generation sequencing in the biological research. The main idea behind it is to construct an automaton over all the pattern strings, and search the automaton against a BWT-array L created for a target string s...
Knowledge extraction from genomic data is important activity for the biologist. In order to extract the underlying biological knowledge, we based on the generic framework of Knowledge extraction from data. In this paper, we transformed DNA sequences into texts, the texts are indexed by TF-IDF and n-grams approach. Secondly, we grouped the similar DNA sequences by clustering; we applied bio-inspired...
This paper presents the comparison between algorithms used to find inexact motifs (transformed into a set of exact sub-sequences) in a DNA sequence. The MFA algorithm builds an automaton that searches for the set of exact sub-sequences by building a finite automaton in a similar way to the KMP algorithm. This algorithm is compared against the traditional automaton using the basic idea of the subset...
A phylogenetic or evolutionary tree is constructed from a set of species or DNA sequences and depicts the relatedness between the sequences. Predictions of future sequences in a phylogenetic tree are important for a variety of applications including drug discovery, pharmaceutical research and disease control. In this work, we predict future DNA sequences in a phylogenetic tree using cellular automata...
Fractals have been used to visually represent biological sequences since 1990. At first simple chaos games were used to generate fractal visualizations for DNA sequences, but the technique developed into using more complex systems to visually represent DNA and protein sequences. One of these more complex systems, termed chaos automata, combined iterated function systems with finite state automata...
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