Abstract: The classical temporal scan statistic is often used to
identify disease clusters. In recent years, this method has become as a
very popular technique and its field of application has been notably
increased. Many bioinformatic problems have been solved with this
technique. In this paper a new scan fuzzy method is proposed. The
behaviors of classic and fuzzy scan techniques are studied with
simulated data. ROC curves are calculated, being demonstrated the
superiority of the fuzzy scan technique.
Abstract: A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represent one or more hypothetical bases with unspecific pairing. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvements of a primitive DNA repair system could make possible the transition from the ancient to the modern genetic code. Our results suggest that the Watson-Crick base pairing and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as the transition from the former to the later. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences.
Abstract: Identifying protein coding regions in DNA sequences is a basic step in the location of genes. Several approaches based on signal processing tools have been applied to solve this problem, trying to achieve more accurate predictions. This paper presents a new predictor that improves the efficacy of three techniques that use the Fourier Transform to predict coding regions, and that could be computed using an algorithm that reduces the computation load. Some ideas about the combination of the predictor with other methods are discussed. ROC curves are used to demonstrate the efficacy of the proposed predictor, based on the computation of 25 DNA sequences from three different organisms.
Abstract: In this paper we designed and implemented a new
ensemble of classifiers based on a sequence of classifiers which were
specialized in regions of the training dataset where errors of its
trained homologous are concentrated. In order to separate this
regions, and to determine the aptitude of each classifier to properly
respond to a new case, it was used another set of classifiers built
hierarchically. We explored a selection based variant to combine the
base classifiers. We validated this model with different base
classifiers using 37 training datasets. It was carried out a statistical
comparison of these models with the well known Bagging and
Boosting, obtaining significantly superior results with the
hierarchical ensemble using Multilayer Perceptron as base classifier.
Therefore, we demonstrated the efficacy of the proposed ensemble,
as well as its applicability to general problems.