title: Prediction of potential barcoding sites on ITS1 by wavelet transform.
abstract: For sustainable development, biodiversity conservation and life-quality improvement must be simultaneously considered. Molecular techniques have greatly impacted biotechnology. These methods have, in particular, improved the capability to investigate the fine differences among organisms and, as a consequence, to better investigate the effects on environmental factors on them. We propose an approach to support the optimal selection of molecular probes for barcoding application in many biotechnological fields. The aim of our work is specificity maximization. To this purpose, we have integrated a filter system based on wavelet transforms with biological knowledge about the sequence proneness to mutation and post-translational modification. Specifically, we have tested the proposed method on ITS1 sequences that are a region of the rRNA locus. Our analysis has shown the presence of other local relative stable conformations in addition to known cleavage site. Their characteristics differ within the group of mammals selected for our analysis. These variations could be used to design new species-specific barcoding probes or other quick molecular screening tools.
authors.affiliation: a DIBRIS - University of Genoa , Genoa , Italy.
authors.forename: Norbert
authors.initials: N
authors.lastname: Maggi
authors.affiliation: a DIBRIS - University of Genoa , Genoa , Italy.
authors.forename: Carmelina
authors.initials: C
authors.lastname: Ruggiero
authors.affiliation: b ISMAC - National Research Council (CNR) , via de Marini, 6, Genoa , Italy.
authors.forename: Patrizio
authors.initials: P
authors.lastname: Arrigo
mesh_terms: D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D058893:DNA Barcoding, Taxonomic / Q000379:methods; D004262:DNA Restriction Enzymes / Q000378:metabolism; D021903:DNA, Ribosomal Spacer; D006801:Humans; D011485:Protein Binding; D058067:Wavelet Analysis
chemical_list: D021903:DNA, Ribosomal Spacer; D004262:DNA Restriction Enzymes
keywords: DNA barcoding; bioinformatics; digital signal processing