A unified approach to word occurrence probabilities

International audienc

Average performance of Morris-Pratt-like algorithms

Résumé disponible dans le fichier PD

Performance of string searching algorithms under various probabilistic models

Résumé disponible dans le fichier PD

A Word Counting Graph

We study methods for counting occurrences of words from a given set H over an alphabet V in a given text. All words have the same length m. Our goal is the computation of the probability to find p occurrences of words from a set H in a random text of size n, assuming that the text is generated by a Bernoulli or Markov model. We have designed an algorithm solving the problem; the algorithm relies on traversals of a graph, whose set of vertices is associated with the overlaps of words from H. Edges define two oriented subgraphs that can be interpreted as equivalence relations on words of H. Let P (H) be the set of equivalence classes and S be the set of other vertices. The run time for the Bernoulli model is O(np(|P (H)| +|S|)) time and the space complexity is O(pm|S| +|P (H)|). In a Markov model of order K, additional space complexity is O(pm|V | K ) and additional time complexity is O(npm|V | K). Our preprocessing uses a variant of Aho-Corasick automaton and achieves O(m|H|) time complexity. Our algorithm is implemented and provides a significant space improvement in practice. We compare its complexity to the additional improvement due to AhoCorasick minimization

Characteristics of binding sites of intergenic, intronic and exonic miRNAs with mRNAs of oncogenes coding intronic miRNAs

International audienceThe interaction of 784 intergenic (ig-miRNA), 686 intronic (in-miRNA) and 49 exonic miRNAs (ex-miRNA) with mRNAs of 51 oncogenes coding in-miRNAs was investigated. Out of the studied genes, 44 were targets for 94 ig-miRNAs, 29 were targets for 44 in-miRNAs and 7 were targets for 7 ex-miRNAs. The density of miRNA binding sites was higher in 5'-untranslated regions than it was in coding sequences and 3'-untranslated regions. Three types of miRNA interaction with mRNA were revealed: 5'-dominant canonical, 3'-compensatory and complementary types. In-miRNAs do not interact with mRNAs of host genes (where in-miRNA is encoded). Linkage between some mRNAs of genes encodes in-miRNAs via other in-miRNAs was revealed. These data promote the understanding of interaction mechanism of miRNA with mRNA genes participating in gastrointestinal and breast cancers.L'interaction de miRNAs avec des mRNAs de 51 incogènes a été étudiée, Trois types d'interaction ont été mis en évidence. Ces données améliorent la compréhension du mécanisme d'interaction des miRNAs avec des gènes mRNAs impliqués dans des cancers de l'intestin ou du sein