Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons

Autor: Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh, Arthur Gruber

Publikováno v: Viruses, Vol 15, Iss 2, p 519 (2023)

Profile hidden Markov models (HMMs) are a powerful way of modeling biological sequence diversity and constitute a very sensitive approach to detecting divergent sequences. Here, we report the development of protocols for the rational design of profil

Externí odkaz: https://doaj.org/article/6ea8278ddac74c389a5349c06d103afc

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Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus–Host Interaction Signatures

Autor: Arthur Gruber, Paula Luize Camargos Fonseca, Aristóteles Góes-Neto, João Trindade Marques, Flávia Gomes Faleiro Ferreira, Felipe Ferreira da Silva, Liliane Santana Oliveira, Eric R.G.R. Aguiar

Publikováno v: Viruses, Vol 13, Iss 9, p 9 (2021)
Viruses
Volume 13
Issue 1
Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP

Hematophagous insects act as the major reservoirs of infectious agents due to their intimate contact with a large variety of vertebrate hosts. Lutzomyia longipalpis is the main vector of Leishmania chagasi in the New World, but its role as a host of

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9565cd3338fdc2b4468d4db86f12d4b8
https://www.mdpi.com/1999-4915/13/1/9

Trypanosoma cruzi defined antigens in the serological evaluation of an outbreak of acute Chagas disease in Brazil (Catolé do Rocha, Paraíba)

Autor: Eufrosina S Umezawa, Maria Aparecida Shikanai-Yasuda, Arthur Gruber, Vera L Pereira-Chioccola, Bianca Zingales

Publikováno v: Memorias do Instituto Oswaldo Cruz, Vol 91, Iss 1, Pp 87-93 (1996)

Immunoglobulin G and M humoral response to recombinant protein B13 and glycoconjugate LPPG Trypanosoma cruzi defined antigens was evaluated by ELISA in 18 patients in the acute phase of Chagas disease, who were contaminated on the same occasion. LPPG

Externí odkaz: https://doaj.org/article/f6dc28a56a4b4a24b227e9adf4c33b5a

A single unidirectional piRNA cluster similar to the flamenco locus is the major source of EVE-derived transcription and small RNAs in Aedes aegypti mosquitoes

Autor: Liliane Santana Oliveira, Eric R.G.R. Aguiar, Lucio Rezende Queiroz, João Trindade Marques, Jean-Luc Imler, Arthur Gruber, Benjamin J. Matthews, Roenick P. Olmo, João Paulo Pereira de Almeida, Isaque João da Silva de Faria

Publikováno v: Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
RNA
RNA, Cold Spring Harbor Laboratory Press, 2020, pp.rna.073965.119. ⟨10.1261/rna.073965.119⟩

Endogenous viral elements (EVEs) are found in many eukaryotic genomes. Despite considerable knowledge about genomic elements such as transposons (TEs) and retroviruses, we still lack information about nonretroviral EVEs. Aedes aegypti mosquitoes have

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::53d94adb72e1071e47cb19271d6d3e9a