Jonathan Perreault

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Estimates of the total number of bacterial species indicate that existing DNA sequence databases carry only a tiny fraction of the total amount of DNA sequence space represented by this division of life. Indeed, environmental DNA samples have been shown to encode many previously unknown classes of proteins and RNAs. Bioinformatics searches of genomic DNA(More)
The RNA of viroids and virusoids in plants, and the RNA transcripts of some tandemly repeated DNA sequences in the newt, can undergo self-catalysed cleavage to generate RNA with 5'-OH and 2',3'-cyclic-phosphate termini. These catalytic RNAs, or ribozymes, form a stem-loop secondary structure called a 'hammerhead' in which the catalytic (ribozyme) and(More)
Hammerhead ribozymes are small self-cleaving RNAs that promote strand scission by internal phosphoester transfer. Comparative sequence analysis was used to identify numerous additional representatives of this ribozyme class than were previously known, including the first representatives in fungi and archaea. Moreover, we have uncovered the first natural(More)
We report the characterization in the human genome of 966 pseudogenes derived from the four human Y (hY) RNAs, components of the Ro/SS-A autoantigen. About 95% of the Y RNA pseudogenes are found in corresponding locations on the chimpanzee and human chromosomes. On the contrary, Y pseudogenes in mice are both infrequent and found in different genomic(More)
We describe here the establishment of an online database containing a large number of sequences and related data on viroids, viroid-like RNAs and human hepatitis delta virus (vHDV) in a customizable and user-friendly format. This database is available on the World Wide Web at http://penelope.med.usherb.ca/subviral.
Mobile genetic elements have significantly contributed to the shaping of mammalian genomes. The RTAnalyzer software tracks sequences of retrotransposed origin by scoring the signature results from an L1-mediated insertion within a genome. More specifically, a sequence of interest is searched for in genomic databases using BLAST. Each hit, along with(More)
A bioinformatic covariation analysis of a collection of 119 novel variants of the antigenomic, self-cleaving hepatitis delta virus (HDV) RNA motif supported the formation of all of the Watson-Crick base pairs (bp) of the catalytic centre except the C19-G81 pair located at the bottom of the P2 stem. In fact, a novel Watson-Crick bp between C19 and G80 is(More)
The Burkholderia cepacia complex (Bcc) comprises strains with a virulence potential toward immunocompromised patients as well as plant growth-promoting rhizobacteria (PGPR). Owing to the link between quorum sensing (QS) and virulence, most studies among Bcc species have been directed toward QS of pathogenic bacteria. We have investigated the QS of B.(More)
Estimates of the total number of bacterial species 1-3 suggest that existing DNA sequence databases carry only a tiny fraction of the total amount of DNA sequence space represented by this division of life. Indeed, environmental DNA samples have been shown to encode many previously unknown classes of proteins 4 and RNAs 5. Bioinformatics searches 6-10 of(More)
Cationic antimicrobial peptides (CAMPs) occur naturally in numerous organisms and are considered as a class of antibiotics with promising potential against multi-resistant bacteria. Herein, we report a strategy that can lead to the discovery of novel small CAMPs with greatly enhanced antimicrobial activity and retained antibiofilm potential. We geared our(More)