108,475 research outputs found
Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family
No full textWagner H, Morgenstern B, Dress A. Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. Algorithms for Molecular Biology. 2008;3(1): 15.Background: Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments. The quality and stability of the underlying alignments is therefore crucial for phylogenetic analysis. Results: In this short report, we investigate alignments and alignment-based phylogenies constructed for a set of 22 ABC transporters using CLUSTAL W and DIALIGN. Comparing the 22 "one-out phylogenies" one can obtain for this sequence set, some intrinsic phylogenetic instability is observed - even if attention is restricted to branches with high bootstrapping frequencies, the so-called safe branches. We show that this instability is caused by the fact that both, CLUSTAL W as well as DIALIGN, apparently get "confused" by sequence repeats in some of the ABC-transporter. To deal with such problems, two new DIALIGN options are introduced that prove helpful in our context, the "exclude-fragment" (or "xfr") and the "self-comparison" (or "sc") option. Conclusion: "One-out strategies", known to be a useful tool for testing the stability of all sorts of data-analysis procedures, can successfully be used also in testing alignment stability. In case instabilities are observed, the sequences under consideration should be carefully checked for putative causes. In case one suspects sequence repeats to be the cause, the new "sc" option can be used to detect such repeats, and the "xfr" option can help to resolve the resulting problems
Sermones disertissimi contra omnem mundi perversum statum ... : quem Deus gloriosus et equitas naturalis damnat
No full textegregii et famosissimi domini Georgii Morgenstern ...Kolophon auf Bl. LXXV recto: "Impressum Auguste per Iohannem Froschauer anno domini 1505."Bogensignaturen: a⁸, a-c⁶, d⁴, e-h⁶, i⁴, k-m⁶, n
AGenDA: gene prediction by cross-species sequence comparison
No full textTaher L, Rinner O, Garg S, Sczyrba A, Morgenstern B. AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research. 2004;32(Web Server):W305-W308.Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprinting: they exploit the fact that functionally important regions in genomic sequences are usually more conserved than non-functional regions. We created a WWW-based software program for homology-based gene prediction at BiBiServ (Bielefeld Bioinformatics Server). Our tool takes pairs of evolutionary related genomic sequences as input data, e.g. from human and mouse. The server runs CHAOS and DIALIGN to create an alignment of the input sequences and subsequently searches for conserved splicing signals and start/stop codons near regions of local sequence conservation. Genes are predicted based on local homology information and splice signals. The server returns predicted genes together with a graphical representation of the underlying alignment. The program is available at http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/
Fast and sensitive multiple alignment of large genomic sequences
No full textBrudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics. 2003;4(1): 66.Background: Genomic sequence alignment is a powerful method for genome analysis and annotation, as alignments are routinely used to identify functional sites such as genes or regulatory elements. With a growing number of partially or completely sequenced genomes, multiple alignment is playing an increasingly important role in these studies. In recent years, various tools for pair-wise and multiple genomic alignment have been proposed. Some of them are extremely fast, but often efficiency is achieved at the expense of sensitivity. One way of combining speed and sensitivity is to use an anchored-alignment approach. In a first step, a fast search program identifies a chain of strong local sequence similarities. In a second step, regions between these anchor points are aligned using a slower but more accurate method. Results: Herein, we present CHAOS, a novel algorithm for rapid identification of chains of local pair-wise sequence similarities. Local alignments calculated by CHAOS are used as anchor points to improve the running time of DIALIGN, a slow but sensitive multiple-alignment tool. We show that this way, the running time of DIALIGN can be reduced by more than 95% for BAC-sized and longer sequences, without affecting the quality of the resulting alignments. We apply our approach to a set of five genomic sequences around the stem-cell-leukemia (SCL) gene and demonstrate that exons and small regulatory elements can be identified by our multiple-alignment procedure. Conclusion: We conclude that the novel CHAOS local alignment tool is an effective way to significantly speed up global alignment tools such as DIALIGN without reducing the alignment quality. We likewise demonstrate that the DIALIGN/CHAOS combination is able to accurately align short regulatory sequences in distant orthologues
Von Neumann-Morgenstern farsightedly stable sets in two-sided matching
No full textWe adopt the notion of von Neumann-Morgenstern (vNM) farsightedly stable sets to determine which matchings are possibly stable when agents are farsighted in one-to-one matching problems. We provide the characterization of vNM farsightedly stable sets: a set of matchings is a vNM farsightedly stable set if and only if it is a singleton subset of the core. Thus, contrary to the vNM (myopically) stable sets [Ehlers, J. of Econ. Theory 134 (2007), 537-547], vNM farsightedly stable sets cannot include matchings that are not in the core. Moreover, we show that our main result is robust to many-to-one matching problems with substitutable preferences: a set of matchings is a vNM farsightedly stable set if and only if it is a singleton set and its element is in the strong core.Matching problem, von Neumann-Morgenstern stable sets, farsighted stability
Aggregating sets of von Neumann-Morgenstern utilities
No full textWe analyze the aggregation problem without the assumption that individuals and society have fully determined and observable preferences. More precisely, we endow individuals ans society with sets of possible von Neumann-Morgenstern utility functions over lotteries. We generalize the classical neutrality assumption to this setting and characterize the class of neutral social welfare function. This class turns out to be considerably broader for indeterminate than for determinate utilities, where it basically reduces to utilitarianism. In particular, aggregation rules may differ by the relationship between individual and social indeterminacy. We characterize several subclasses of neutral aggregation rules and show that utilitarian rules are those that yield the least indeterminate social utilities, although they still fail to systematically yield a determinate social utility.Aggregation; vNM utility; indeterminacy; neutrality; utilitarianism
Extended paretian rules and relative utilitarianism
No full textThis paper introduces the 'Extended Pareto' axiom on Social welfare functions and gives a characterization of the axiom when it is assumed that the Social Welfare Functions that satisfy it in a framework of preferences over lotteries also satisfy the restrictions (on the domain and range of preferences) implied by the von-Neumann-Morgenstern axioms. With the addition of two other axioms: Anonymity and Weak IIA* it is shown that there is a unique Social Welfare Function called Relative Utilitarianism that consists of normalizing individual utilities between zero and one and then adding them
The Collapse of Interwar Vienna: Oskar Morgenstern’s Community, 1925 - 1950
No full textFrom the perspective of science, art and intellectual life in general, Interwar Vienna was one of the most vibrant communities in modern European history. Within the field of economics, it was home to, amongst others, Ludwig von Mises, Friedrich von Hayek, Hans Mayer, Gottfried Haberler, Fritz Machlup, Oskar Morgenstern, Karl Menger and Abraham Wald. The community flourished after the end of World War I, and then began to suffer in the early 1930’s as a result of growing political instability and rising anti-semitism. With the Anschluss of Austria by the Third Reich in March 1938, it collapsed completely, never to recover. Drawing on the personal papers of two key participants, Oskar Morgenstern and Karl Menger, and also on the archives of the Rockefeller Foundation, this paper provides a portrait of that community, chronicling its evolution and dramatic collapse. Particular attention is paid to the milieu surrounding Morgenstern, both as director of the Rockefeller-funded Austrian Institute for Business Cycle Research and as philosophical “dissident”. In collaborating with mathematicians Menger, Wald and, later, John von Neumann, he gradually forsook his Austrian theoretical legacy. The account detailed here shows conflict and tension to have been central to both the life and death of this fabled community.
Decision under risk : The classical Expected Utility model
No full textThis chapter of a collective book aims at presenting the basics of decision making under risk. We first define notions of risk and increasing risk and recall definitions and classifications (that are valid independently of any representation) of behavior under risk. We then review the classical model of expected utility due to von Neumann and Morgenstern andd its main properties. Issues raised by this model are then discussed and two models generalizing the expected utility model are briefly discussed.Risk, risk aversion, expected utility, von Neumann and Morgenstern, Allais paradox.
Von Neumann–Morgenstern Hypergraphs
No full textA simple hypergraph H with vertex set X and edge set E is representable by Von Neumann–Morgenstern (VNM)-stable sets—or VNM—if there exists an irreflexive simple digraph D with vertex set X such that each edge of H is a VNM-stable set of D. It is shown that a simple hypergraph H is VNM if and only if each edge of H is a maximal clique of the conjugation graph of H. A related algorithm that identifies finite VNM hypergraphs is also provided
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