10 documents found, page 1 of 1
Concentration of inverted repeats along human DNA
Bastos, Carlos A. C.; Afreixo, Vera; Rodrigues, João M. O. S.; Pinho, Armando J.This work aims to describe the observed enrichment of inverted repeats in the human genome; and to identify and describe, with detailed length profiles, the regions with significant and relevant enriched occurrence of inverted repeats. The enrichment is assessed and tested with a recently proposed measure (z-scores based measure). We simulate a genome using an order 7 Markov model trained with the data from the...
Detection and characterization of local inverted repeats regularities
Bastos, Carlos A. C.; Afreixo, Vera; Rodrigues, João M. O. S.; Pinho, Armando J.To explore the inverted repeats regularities along the genome sequences, we propose a sliding window method to extract the concentration scores of inverted repeats periodic regularities and the total mass of possible inverted repeats pairs. We apply the method to the human genome and locate the regions with the potential for the formation of large number of hairpin/cruciform structures. The number of found wind...
Distribution of distances between symmetric words in the human genome: analysis...
Bastos, Carlos A. C.; Afreixo, Vera; Rodrigues, João M. O. S.; Pinho, Armando J.; Silva, Raquel M.Finding DNA sites with high potential for the formation of hairpin/cruciform structures is an important task. Previous works studied the distances between adjacent reversed complement words (symmetric word pairs) and also for non-adjacent words. It was observed that for some words a few distances were favoured (peaks) and that in some distributions there was strong peak regularity. The present work extends prev...
An analysis of symmetric words in human DNA: adjacent vs non-adjacent word dist...
Bastos, Carlos A. C.; Afreixo, Vera; Rodrigues, João M. O. S.; Pinho, Armando J.It is important to develop methods for nding DNA sites with high potencial for the formation of hairpin/cruciform structures. In a previous work, we studied the distances between adjacent reversed complement words (symmetric words), and we observed that for some words some distances were favored. In the work presented here, we extended the study to the distance between non-adjacent reversed complement words and...
Comparing reverse complementary genomic words based on their distance distribut...
Tavares, Ana Helena; Raymaekers, Jakob; Rousseeuw, Peter J.; Silva, Raquel M.; Bastos, Carlos A. C.; Pinho, Armando; Brito, Paula; Afreixo, VeraIn this work, we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very d...
DNA word analysis based on the distribution of the distances between symmetric ...
Tavares, Ana Helena; Pinho, Armando J.; Silva, Raquel M.; Rodrigues, João M. O. S.; Bastos, Carlos A. C.; Ferreira, Paulo J. S. G.; Afreixo, VeraWe address the problem of discovering pairs of symmetric genomic words (i.e., words and the corresponding reversed complements) occurring at distances that are overrepresented. For this purpose, we developed new procedures to identify symmetric word pairs with uncommon empirical distance distribution and with clusters of overrepresented short distances. We speculate that patterns of overrepresentation of short ...
Dissimilar symmetric word pairs in the human genome
Tavares, Ana Helena; Raymaekers, Jakob; Rousseeuew, Peter; Silva, Raquel M.; Bastos, Carlos A. C.; Pinho, Armando; Brito, Paula; Afreixo, VeraIn this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the comple...
Analysis of single-strand exceptional word symmetry in the human genome: new me...
Afreixo, Vera; Rodrigues, João M. O. S.; Bastos, Carlos A. C.Some previous studies suggest the extension of Chargaff's second rule (the phenomenon of symmetry in a single DNA strand) to long DNA words. However, in random sequences generated under an independent symbol model where complementary nucleotides have equal occurrence probabilities, we expect the phenomenon of symmetry to hold for any word length. In this work, we develop new statistical methods to measure the e...
Segmentation of DNA into coding and noncoding regions based on inter-STOP symbo...
Bastos, Carlos A. C.; Afreixo, Vera; Garcia, Sara P.; Pinho, Armando J.In this study we set to explore the potentialities of the inter-genomic symbols distance for finding the coding regions in DNA sequences. We use the distance between STOP symbols in the DNA sequence and a chi-square statistic to evaluate the nonhomogeneity of the three possible reading frames. The results of this exploratory study suggest that inter-STOP symbols distance has strong ability to discriminate codin...
On the representability of complete genomes by multiple competing finite-contex...
Pinho, Armando J.; Ferreira, Paulo J. S. G.; Neves, António J. R.; Bastos, Carlos A. C.A finite-context (Markov) model of order k yields the probability distribution of the next symbol in a sequence of symbols, given the recent past up to depth k. Markov modeling has long been applied to DNA sequences, for example to find gene-coding regions. With the first studies came the discovery that DNA sequences are non-stationary: distinct regions require distinct model orders. Since then, Markov and hidd...