Electrophoretic data classification for phylogenetics and biostatistics

Cardinali, Gianluigi; Maraziti, Francesco; Selvi, S.

doi:10.1093/bioinformatics/btg294

Cited by 6 publications

(3 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, problems may arise when combining different types of data (Cardinali et al 2002) and efficient algorithms are needed for nonsubjective classification of continuous data (e.g. the molecular weights of the RAPD bands) in binary matrices (Cardinali and Martini 1999;Rementeria et al 2001Rementeria et al , 2004Cardinali et al 2003). The results presented in this study show that increasing the number of descriptors improves the discrimination of strains with a clear effect of saturation because discrimination of the most similar strains requires many more descriptors than the differentiation of the least similar strains.…”

Section: Discussionmentioning

confidence: 99%

Use of RAPD and killer toxin sensitivity in Saccharomyces cerevisiae strain typing

et al. 2005

Self Cite

View full text Add to dashboard Cite

Aims: Two different strain characterization techniques, random amplified polymorphic DNA (RAPD) and killer toxin sensitivity (KTS), were compared to assess their typing performance using a set of 30 certified Saccharomyces cerevisiae strains. Methods and Results: A sequential random resampling procedure was employed to subdivide the 32 descriptors in eight sets, in order to compare the differential performances of the two techniques with diverse number of characters. Results showed that RAPD performs better than killer, although the complete differentiation of the strains under study could be obtained only by combining profiles from the two techniques Conclusions: The combination of different typing techniques was useful when discriminating similar organisms. In such cases, the introduction of a second typing technique can be more advantageous than increasing the number of characters obtained with a single method. Significance and Impact of the Study: The distribution of among-strains pairwise distances and the relative performance of the two techniques has implications for the study of biodiversity, taxonomy and microbial ecology.

show abstract

Section: Discussionmentioning

confidence: 99%

Use of RAPD and killer toxin sensitivity in Saccharomyces cerevisiae strain typing

et al. 2005

Self Cite

View full text Add to dashboard Cite

show abstract

“…(GACA) 4 i-SSR and RAPD profiles were converted in binary (0/1) matrixes with the ClassMaker 1.27 software (Cardinali et al, 2003), following the procedures described in the paper and with an additional check that similar bands were included in the same band class. Euclidean distances among the strains were calculated from the binary matrices and used to build the DIANA tree with the Cluster Package (Kaufman and Rousseeuw, 1990) in the R statistical environment.…”

Section: I-ssr (Gaca) 4 and Rapd Analysismentioning

confidence: 99%

Phenotypic and molecular diversity of Meyerozyma guilliermondii strains isolated from food and other environmental niches, hints for an incipient speciation

et al. 2015

View full text Add to dashboard Cite

“…In order to test the proposed methods in a real situation, we considered a binary matrix with 13 descriptors obtained applying a previously published classification method (Cardinali Bioinformatics 2003) [8] to RAPD profiles of 26 yeast isolates ( Table 3).…”

Section: A Real-world Validationmentioning

confidence: 99%

ESTHER: A “R Package” Implementing a Novel Approach to Bidimen-sional Display of Multidimensional Binary Data

Cardinali¹,

Antonielli²,

Rellini³

et al. 2007

TOAINFOJ

Self Cite

View full text Add to dashboard Cite

Abstract:The R package ESTHER implements two novel algorithms designed to dispose in a reduced space multidimensional objects defined by binary descriptors. The approach is to assign discrete and fix positions to all possible combinations obtained with the descriptors employed. One of the two algorithms, called clock, position objects on a circle at regular intervals, whereas the other, star, maintains the angular position as in clock, but defines the distance of the object from the center of the circle proportionally to the number of descriptor in state"1". Comparisons with Principal Coordinate Analysis (PCoA) showed that the three methods perform differently according to the number of objects and descriptors and to the distance method employed to carry out the PCoA. The algorithm clock produced the best object clustering in a validation carried out with a matrix generated by molecular fingerprint of yeast isolates.

show abstract

Electrophoretic data classification for phylogenetics and biostatistics

Abstract: ClassMaker is freely available from http://www.agr.unipg.it/cardinali/index.html, where a list of the URLs from which programs of image analysis, statistics and phylogenetics can be freely downloaded.

Cited by 6 publications

References 8 publications

Use of RAPD and killer toxin sensitivity in Saccharomyces cerevisiae strain typing

Use of RAPD and killer toxin sensitivity in Saccharomyces cerevisiae strain typing

Phenotypic and molecular diversity of Meyerozyma guilliermondii strains isolated from food and other environmental niches, hints for an incipient speciation

ESTHER: A “R Package” Implementing a Novel Approach to Bidimen-sional Display of Multidimensional Binary Data

Contact Info

Product

Resources

About