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- Keyword
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- Sequence Alignment and Phylogenetics (2)
- Chess (1)
- Clustal; DNA sequence alignment; Evolutionary distance; Gap character coding; Homology; Indel; Parsimony; Simulation; Tree reconstruction (1)
- ClustalW; direct optimization; multiple sequence alignment; parsimony; phylogenetics; POY; sensitivity analysis; simulation; tree reconstruction (1)
- Data bases (1)
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Articles 1 - 5 of 5
Full-Text Articles in Genetics and Genomics
Identification Of Synechococcus Sp. Iu 625 Metallothionein Gene And Its Evolutionary Relationship To The Metallothionein Gene Of Other Cyanobacteria, Tin-Chun Chu, Lee Lee, John Gaynor, Quinn Vega, Bonnie Lustigman, Shankar Srinivasan
Identification Of Synechococcus Sp. Iu 625 Metallothionein Gene And Its Evolutionary Relationship To The Metallothionein Gene Of Other Cyanobacteria, Tin-Chun Chu, Lee Lee, John Gaynor, Quinn Vega, Bonnie Lustigman, Shankar Srinivasan
Tin-Chun Chu, Ph.D.
No abstract provided.
Genome-Wide Patterns Of Nucleotide Polymorphism In Domesticated Rice, Ana Lucia Caicedo, S. H. Williamson, R, D. Hernandez, A. Boyko, A. Fleded-Alon, T. L. York, N. Polato, K. M. Olsen, R. Nielsen, S. Mccouch, C. D. Bustamante, M. D. Purugganan
Genome-Wide Patterns Of Nucleotide Polymorphism In Domesticated Rice, Ana Lucia Caicedo, S. H. Williamson, R, D. Hernandez, A. Boyko, A. Fleded-Alon, T. L. York, N. Polato, K. M. Olsen, R. Nielsen, S. Mccouch, C. D. Bustamante, M. D. Purugganan
Ana Lucia Caicedo
Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns …
Chess, Chance And Conspiracy, Mark Segal
Chess, Chance And Conspiracy, Mark Segal
Mark R Segal
Chess and chance are seemingly strange bedfellows. Luck and/or randomness have no apparent role in move selection when the game is played at the highest levels. However, when competition is at the ultimate level, that of the World Chess Championship (WCC), chess and conspiracy are not strange bedfellows, there being a long and colorful history of accusations levied between participants. One such accusation, frequently repeated, was that all the games in the 1985 WCC (Karpov vs Kasparov) were fixed and prearranged move by move. That this claim was advanced by a former World Champion, Bobby Fischer, argues that it ought …
Does Direct Optimization Produce More Accurate Alignments And Topologies? Poy Vs. Clustalw+Paup*, T. Heath Ogden
Does Direct Optimization Produce More Accurate Alignments And Topologies? Poy Vs. Clustalw+Paup*, T. Heath Ogden
T. Heath Ogden
Direct optimization frameworks for simultaneously estimating alignments and phylogenies have recently been developed. One such method, implemented in the program POY, is becoming more common for analyses of variable length sequences (e.g., analyses using ribosomal genes) and for combined evidence analyses (morphology + multiple genes). Simulation of sequences containing insertion and deletion events was performed in order to directly compare a widely used method of multiple sequence alignment (ClustalW) and subsequent parsimony analysis in PAUP* with direct optimization via POY. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (clocklike, non-clocklike, and ultrametric). Alignment accuracy …
How Should Gaps Be Treated In Parsimony? A Comparison Of Approaches Using Simulation, T. Heath Ogden
How Should Gaps Be Treated In Parsimony? A Comparison Of Approaches Using Simulation, T. Heath Ogden
T. Heath Ogden
Simulation with indels was used to produce alignments where true site homologies in DNA sequences were known; the gaps from these datasets were removed and the sequences were then aligned to produce hypothesized alignments. Both alignments were then analyzed under three widely used methods of treating gaps during tree reconstruction under the maximum parsimony principle. With the true alignments, for many cases (82%), there was no diVerence in topological accuracy for the diVerent methods of gap coding. However, in cases where a diVerence was present, coding gaps as a Wfth state character or as separate presence/absence characters outperformed treating gaps …