A perceptual hash function to store and retrieve large scale DNA sequences

This paper proposes a novel approach for storing and retrieving massive DNA sequences.. The method is based on a perceptual hash function, commonly used to determine the similarity between digital images, that we adapted for DNA sequences. Perceptual hash function presented here is based on a Discrete Cosine Transform Sign Only (DCT-SO). Each nucleotide is encoded as a fixed gray level intensity pixel and the hash is calculated from its significant frequency characteristics. This results to a drastic data reduction between the sequence and the perceptual hash. Unlike cryptographic hash functions, perceptual hashes are not affected by "avalanche effect" and thus can be compared. The similarity distance between two hashes is estimated with the Hamming Distance, which is used to retrieve DNA sequences. Experiments that we conducted show that our approach is relevant for storing massive DNA sequences, and retrieving them

Indexation d'une grande quantité de séquences ADN dans une base de données NOSQL à l'aide d'algorithmes de hachage perceptuel

National audienc

Indexation de séquences d'ADN dans une base de données NoSQL à l'aide d'algorithmes de hachage perceptuel

National audienc

A perceptual hash algorithm for indexing and similarity search in a database of DNA sequence

National audienc

Stockage, indexation et comparaison d’une grande quantité de données génomiques à l’aide d’algorithmes de traitement d’images dans un environnement d’exécution NoSQL et GPU

National audienc

Surveillance de l'infection équine à virus West Nile en France : bilan 2000-2007

National audienceWest Nile fever is a mosquito-borne virosis involving wild birds as amplifying hosts, and humans and horses as highly susceptible and incidental hosts. Outbreaks of West Nile fever have already been reported in metropolitan France, in the Camargue region from 1962 to 1965. After 35 years without any evidence of viral transmission, West Nile fever has been reported again in 2000 in horses in the Camargue region. Following this outbreak, passive surveillance of equine encephalomyelitis has been reinforced in French departments, particularly in those bordering the Mediterranean. This surveillance led to the identification of 4 distinct outbreaks of West Nile fever, responsible for neurological illnesses in horses, in the Camargue region in 2000 and 2004, in the Var department in 2003 and in eastern Pyrenees in 2006. This equine surveillance system thus allowed sensitive detection of hot-spots of viral amplification in these regions, and could be reinforced by a syndromic surveillance protocol to facilitate earlier detection. The situation in the French West Indies is in many respects different from that in metropolitan France, but the need for West Nile virus surveillance has been underscored by the rapid spread and increased virulence of the virus that was introduced onto the American continent. In this context, an active surveillance system based on regular serological controls of the equine population was useful in demonstrating active viral transmission in Guadeloupe in 2002 and 2003, without any recorded human or equine clinical cases. Results obtained by surveillance in metropolitan France, Guadeloupe and Martinique between 2000 and 2007 are presented.La fièvre de West Nile est une virose transmise par les moustiques dont les oiseaux sauvages sont les hôtes amplificateurs et le cheval et l’homme des hôtes accidentels particulièrement sensibles. Le virus avait déjà circulé en France métropolitaine, dans la région de la Camargue entre 1962 et 1965. Après un silence de plus de 35 ans, la maladie a été décrite à nouveau chez le cheval en 2000, dans la région de la grande Camargue. A la suite de cet épisode, la surveillance passive des encéphalomyélites dans l’espèce équine a été renforcée, en particulier dans les départements du pourtour méditerranéen, et a permis d’identifier quatre épisodes distincts de circulation du virus West Nile, associés à des cas cliniques chez le cheval : en Camargue, en 2000 et 2004, dans le Var en 2003 ainsi que dans les Pyrénées-Orientales en 2006. Elle a donc permis de détecter de façon sensible les foyers de circulation et d’amplification intense du virus West Nile dans ces régions et pourrait être renforcée par un protocole de surveillance syndromique dans le but d’améliorer encore la précocité du système d’alerte équin. La situation dans les départements français des Antilles est bien différente, mais la nécessité d’une surveillance du virus s’est imposée très rapidement devant l’extension géographique rapide et la virulence du virus West Nile introduit sur le continent américain : un système actif, faisant appel à des analyses sérologiques régulières de la population équine, a permis de démontrer une circulation virale active en Guadeloupe en 2002 et 2003, sans qu’aucun cas clinique humain ou équin ne soit décrit. Un bilan des résultats de surveillance obtenus en métropole, en Guadeloupe et Martinique entre 2000 et 2007 est dressé

Indexation et comparaison de séquences ADN à partir d'une fonction de hachage perceptuel

National audienc

Web monitoring of emerging animal infectious diseases integrated in the French Animal Health Epidemic Intelligence System

Since 2013, the French Animal Health Epidemic Intelligence System (in French: Veille Sanitaire Internationale, VSI) has been monitoring signals of the emergence of new and exotic animal infectious diseases worldwide. Once detected, the VSI team verifies the signals and issues early warning reports to French animal health authorities when potential threats to France are detected. To improve detection of signals from online news sources, we designed the Platform for Automated extraction of Disease Information from the web (PADI-web). PADI-web automatically collects, processes and extracts English-language epidemiological information from Google News. The core component of PADI-web is a combined information extraction (IE) method founded on rule-based systems and data mining techniques. The IE approach allows extraction of key information on diseases, locations, dates, hosts and the number of cases mentioned in the news. We evaluated the combined method for IE on a dataset of 352 disease-related news reports mentioning the diseases involved, locations, dates, hosts and the number of cases. The combined method for IE accurately identified (F-score) 95% of the diseases and hosts, respectively, 85% of the number of cases, 83% of dates and 80% of locations from the disease-related news. We assessed the sensitivity of PADI-web to detect primary outbreaks of four emerging animal infectious diseases notifiable to the World Organisation for Animal Health (OIE). From January to June 2016, PADI-web detected signals for 64% of all primary outbreaks of African swine fever, 53% of avian influenza, 25% of bluetongue and 19% of foot-and-mouth disease. PADI-web timely detected primary outbreaks of avian influenza and foot-and-mouth disease in Asia, i.e. they were detected 8 and 3 days before immediate notification to OIE, respectively