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S Wyman

Publications and source records attributed to S Wyman.

4 recordsLinked to original sources
PubMed2001

A new implementation and detailed study of breakpoint analysis.

Phylogenies derived from gene order data may prove crucial in answering some fundamental open questions in biomolecular evolution. Yet very few techniques are available for such phylogenetic reconstructions. One method is breakpoint analysis, developed by Blanchette and Sankoff for solving the "breakpoint phylogeny." Our earlier studies confirmed the usefulness of this approach, but also found that BPAnalysis, the implementation developed by Sankoff and Blanchette, was too slow to use on all but very small datasets. We report here on a reimplementation of BPAnalysis using the principles of algorithmic engineering. Our faster (by 2 to 3 orders of magnitude) and flexible implementation allowed us to conduct studies on the characteristics of breakpoint analysis, in terms of running time, quality, and robustness, as well as to analyze datasets that had so far been considered out of reach. We report on these findings and also discuss future directions for our new implementation.

Algorithms↗
PubMed2000

A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data.

The breakpoint phylogeny is an optimization problem proposed by Blanchette et al. for reconstructing evolutionary trees from gene order data. These same authors also developed and implemented BPAnalysis [3], a heuristic method (based upon solving many instances of the travelling salesman problem) for estimating the breakpoint phylogeny. We present a new heuristic for this purpose; although not polynomial-time, our heuristic is much faster in practice than BPAnalysis. We present and discuss the results of experimentation on synthetic datasets and on the flowering plant family Campanulaceae with three methods: our new method, BPAnalysis, and the neighbor-joining method [25] using several distance estimation techniques. Our preliminary results indicate that, on datasets with slow evolutionary rates and large numbers of genes in comparison with the number of taxa (genomes), all methods recover quite accurate reconstructions of the true evolutionary history (although BPAnalysis is too slow to be practical), but that on datasets where the rate of evolution is high relative to the number of genes, the accuracy of all three methods is poor.

Algorithms↗
PubMed1990

Optimal conditions for synthesizing complementary DNA in the HIV-1 endogenous reverse transcriptase reaction.

Concentration of monovalent and divalent cations, anionic detergent, reducing agent and nucleotides, as well as pH, temperature, and incubation time were optimized for high levels of HIV-1 endogenous reverse transcriptase activity. In addition, mellitin, a peptide substitute for anionic detergent, and oligo(dT)12-18 were found to stimulate nucleic acid synthesis. This HIV-1 endogenous reaction demonstrated RNA- and DNA-dependent DNA polymerase activities. Nucleic acid intermediates and final products included RNA:DNA hybrids as well as single- and double-stranded DNA. The complementary DNA products formed were representative of all regions of the HIV-1 genome.

Cations↗