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BAG. Journal of basic and applied genetics

On-line version ISSN 1852-6233


BRUNO, C.; ARROYO, A.; GIMENEZ PECCI, M. P.  and  BALZARINI, M.. Comparación de ordenaciones de muestras a nivel de secuencias de aminoácidos, nucleótidos y marcadores RFLP. BAG, J. basic appl. genet. [online]. 2007, vol.18, n.1, pp.39-49. ISSN 1852-6233.

Between-sample distances obtained from nucleotide and aminoacid sequences as well as from DNA marker data are frequent in Molecular Biology. Multidimensional Scaling (MDS) is a statistical technique that allows to explore the underlying relationship among samples via graphical representation of the matrix containing the distances among samples. With m samples evaluated at p nucleotide, p aminoacids or p molecular markers, MDS uses a distance matrix Dm×m as input, providing a system of new axes so as to order the m samples in planes. We ordered four viral cDNA samples through MDS applied to different distance matrixes: Jones-Taylor-Thornton (distance among protein sequences), Felsenstein84 (distance among nucleotide sequences), square root of complement to one of the identity scores obtained during multiple alignment of aminoacid and nucleotide sequences, and square root of complement to one of Dice´s and Simple Matching similarity coefficients among RFLP profiles. A new version of MDS is proposed to simultaneously show ordinations from different types of genomic data. The bidimensional ordinations of the viral samples obtained from different distance models were compared by Procrustes rotation and a consensus ordination was obtained.

Keywords : Euclidean distance; Metric multidimensional scaling; Procrustes rotation; Mal de Río Cuarto virus.

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