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检索条件"任意字段=Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004"

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Efficient reconstruction of phylogenetic networks with constrained recombination 2

Efficient reconstruction of phylogenetic networks with const...

引用

2nd International computational systems bioinformatics conference

作者： Gusfield, D Eddhu, S Langley, C Univ Calif Davis Dept Comp Sci Davis CA 95616 USA

ISBN: (纸本)0769520006

A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not treelike. With the growth of genomic data, much of which does not fit ideal tree models, there is greater need to understand the algorithmics and combinatorics of phylogenetic networks [10, 11]. However, to date, very little has been published on this, with the notable exception of the paper by Wang et al.[12]. Other related papers include [4, 5, 7] We consider the problem introduced in [12], of determining whether the sequences can be derived on a phylogenetic network where the recombination cycles are node disjoint. In this paper, we call such a phylogenetic network a "galled-tree". By more deeply analysing the combinatorial constraints on cycle-disjoint phylogenetic networks, we obtain an efficient algorithm that is guaranteed to be both a necessary and sufficient test for the existence of a galled tree for the data. If there is a galled-tree, the algorithm constructs one and obtains an implicit representation of all the galled trees for the data, and can create these in linear time for each one. We also note two additional results related to galled trees: first, any set of sequences that can be derived on a galled tree can be derived on a true tree (without recombination cycles), where at most one back mutation is allowed per site;second, the site compatibility problem (which is NP-hard in general) can be solved in linear time for any set of sequences that can be derived on a galled tree. The combinatorial constraints we develop apply (for the most part) to node-disjoint cycles in any phylogenetic network (not just galled-trees), and can be used for example to prove that a given site cannot be on a node-disjoint cycle in any phylogenetic network. Perhaps more important than the specific results about galled-trees, we introduce an approach that can be used to study recombination in phylogenetic networks that go beyond galled-trees.

关键词： bioinformatics

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Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance

Prokaryote phylogeny without sequence alignment: from avoida...

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ieee conference on bioinformatics

作者： Bailin Hao Ji Qi T-Life Research Center Fudan University Shanghai China Institute of Theoretical Physics Chinese Academy and Sciences Beijing China

ISBN: (纸本)0769520006

A new and essentially simple method to reconstruct prokaryotic phylogenetic trees from their complete genome data without using sequence alignment is proposed. It is based on the appearance frequency of oligopeptides of a fixed length (up to K=6) in their proteomes. This is a method without fine adjustment and choice of genes. It can incorporate the effect of lateral gene transfer to some extent and leads to results comparable with the bacteriologists' systematics as reflected in the latest 2001 edition of the Sergey's manual of systematic bacteriology. A key point in our approach is subtraction of a random back-groundby using a Markovian model of order K-1 from the composition vectors to highlight the shaping role of natural selection.

关键词： Phylogeny bioinformatics Genomics Microorganisms Systematics Sequences Frequency Organisms Archaea Physics

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Molecular evaluation using comparative molecular interaction profile analysis system

Molecular evaluation using comparative molecular interaction...

引用

ieee conference on bioinformatics

作者： Y. Hayashi K. Sakaguchi N. Iwata M. Kobayashi KLIMERS Co. LTD Toyohashi University of Technology KLIMERS Co. LTD Japan

Creating a new molecular description factor based on the results of computational docking study will add new dimensions in molecular evaluation. We propose a new molecular description factor analysis system named comparative molecular interaction profile analysis system (CoMIPA) in which the AutoDock program is used for docking evaluation of small molecule compound-protein complexes. Interaction energies are calculated, and the data sets obtained are named interaction profiles (IPFs). Using IPF as a scoring indicator, the system could be a powerful tool to cluster the interacting properties between small molecules and bio macromolecules such as ligand-receptor bindings. The system can use computational molecular docking results to explain biological events such as adverse drug reactions and possibly other unforeseen interactions caused by environmental hormones. We believe that the system has the potential to be a major stepping-stone for bridging computational science and biology.

关键词： Engines Proteins bioinformatics Graphics Tree graphs Databases Drugs Biology Computer displays Chemistry

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Algorithms for bounded-error correlation of high dimensional data in microarray experiments

Algorithms for bounded-error correlation of high dimensional...

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ieee conference on bioinformatics

作者： M. Koyuturk A. Grama W. Szpankowski Department of Computer Sciences Purdue University West Lafayette IN USA

The problem of clustering continuous valued data has been well studied in literature. Its application to microarray analysis relies on such algorithms as k-means, dimensionality reduction techniques, and graph-based approaches for building dendrograms of sample data. In contrast, similar problems for discrete-attributed data are relatively unexplored. An instance of analysis of discrete-attributed data arises in detecting co-regulated samples in microarrays. In this paper, we present an algorithm and a software framework, PROXIMUS, for error-bounded clustering of high-dimensional discrete attributed datasets in the context of extracting co-regulated samples from microarray data. We show that PROXIMUS delivers outstanding performance in extracting accurate patterns of gene-expression.

关键词： bioinformatics

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Microbial functional genomics: pulling together a variety of approaches and concepts

Microbial functional genomics: pulling together a variety of...

引用

ieee conference on bioinformatics

作者： J.-M. Claverie Institut de Biologie Structurale et Microbiologie Marseilles France

With the human and mouse genome sequences behind us, whole microbial genome sequencing has become the most active area in genomics today. As easy targets have been worked on first, the microbes under scrutiny today are frequently uncharacterized and difficult to grow and isolate. In those cases, genome sequences often constitute the first and only reliable information about the microorganism to which they belong. It also becoming the rule that no experiments (genetics, transformation, mutagenesis) are directly possible on the microorganism. For better characterized microbes, the competition in the field pushes us to get interested in "anonymous genes" for which no functional clues have be gained from routine sequence analysis.

关键词： Genomics bioinformatics Laboratories Microorganisms Humans Mice Genetics Collaborative work Throughput Protein engineering

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A contradiction-based framework for testing gene regulation hypotheses

A contradiction-based framework for testing gene regulation ...

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ieee conference on bioinformatics

作者： S. Racunas N. Shah N.V. Fedoroff Pennsylvania State University USA

We have developed a mathematical framework for representing and testing hypotheses about gene, protein, and signaling molecule interactions. It takes a hierarchical, contradiction-based approach, and can make use of multiple data sources to assess hypothesis viability and to generate a viability partial order over the space of hypotheses. We have developed an event-based formal language for the expression of such hypotheses. This language seamlessly integrates regulatory diagrams (graphical inputs) and structured English (text input) to maximize flexibility. We have developed a pre-topological formalism that allows us to make precise statements about hypothesis similarity and the convergence of iterative refinements of a base hypothesis. To this, we add mathematical machinery that allows us to make precise statements about control and regulation.

关键词： Testing Biological processes Biological systems Filters bioinformatics Biology computing Character generation Protein engineering Formal languages Natural languages

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An SVM-based algorithm for identification of photosynthesis-specific genome features

An SVM-based algorithm for identification of photosynthesis-...

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ieee conference on bioinformatics

作者： G.-X. Yu G. Ostrouchov A. Geist N.F. Samatova Computational Biology Group Computer Science and Mathematics Division Oak Ridge National Laboratory Oak Ridge TN USA

This paper presents a novel algorithm for identification and functional characterization of "key" genome features responsible for a particular biochemical process of interest. The central idea is that individual genome features are identified as "key" features if the discrimination accuracy between two classes of genomes with respect to a given biochemical process is sufficiently affected by the inclusion or exclusion of these features. In this paper, genome features are defined by high-resolution gene functions. The discrimination procedure utilizes the support vector machine classification technique. The application to the oxygenic photosynthetic process resulted in 126 highly confident candidate genome features. While many of these features are well-known components in the oxygenic photosynthetic process, others are completely unknown, even including some hypothetical proteins. It is obvious that our algorithm is capable of discovering features related to a targeted biochemical process.

关键词： Genomics bioinformatics Organisms computational biology Computer science Mathematics Laboratories Genetics Pathogens Proteins

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The approximate algorithm for analysis of the strand separation transition in superhelical DNA using nearest neighbor energetics

The approximate algorithm for analysis of the strand separat...

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ieee conference on bioinformatics

作者： C. Bi C.J. Benham UC Davis Genome Center University of California Davis CA USA

We present a computational method to analyze the propensity of superhelically stressed DNA to undergo strand separation events, as is required for the initiation of both transcription and replication. We build in silico models to analyze the statistical mechanical equilibrium distribution of a population of identical, stressed DNA molecules among its states of strand separation. In this phenomenon, which we call stress induced duplex destabilization (SIDD), a state energy is determined by the energy cost of opening the specific separated base pairs in that state, and the energy relief from the relaxation of stress this affords. We use experimentally measured values of all energy parameters, including the nearest neighbor energetics known to govern DNA base pair stability. We perform a statistical mechanical analysis in which the approximate equilibrium distribution is calculated from all states whose free energies do not exceed a user-defined threshold. This provides the most general and efficient computational approach to the analysis of this phenomenon. The algorithm is implemented in C++.

关键词： Approximation algorithms Algorithm design and analysis Nearest neighbor searches DNA computing bioinformatics

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Fold recognition using sequence fingerprints of protein local substructures

Fold recognition using sequence fingerprints of protein loca...

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ieee conference on bioinformatics

作者： A. Kryshtafovych T.R. Hvidsten J. Komorowski K. Fidelis Lawrence Livermore National Laboratories Livermore CA USA The Linnaeus Centre for Bioinformatics University of Uppsala Uppsala Sweden

A protein local substructure (descriptor) is a set of several short nonoverlapping fragments of the polypeptide chain. Each substructure describes local environment of a particular residue and includes only those segments of the main chain that are located in the proximity of that residue. Similar descriptors from the representative set of proteins were analyzed to reveal links between the substructures and the sequences of their segments. Using the detected sequence-based fingerprints, specific geometrical conformations are assigned to new sequences. The ability of the approach to recognize correct SCOP folds was tested on 273 sequences from the 49 most popular folds. Good predictions were obtained in 85% of cases. No performance drop was observed with decreasing sequence similarity between target sequences and sequences from the training set of proteins.

关键词： Fingerprint recognition Libraries Shape Assembly Protein engineering Amino acids Laboratories bioinformatics Testing Prediction methods

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A query language to support scientific discovery

A query language to support scientific discovery

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ieee conference on bioinformatics

作者： B. Eckman K. Deutsch M. Janer Z. Lacroix L. Raschid IBM Life Sciences West Chester PA USA Institute for system Biology Seattle WA USA Arizona State University Tempe AZ USA University of Maryland College Park MD USA

Traditional data management approaches need to be leveraged to support scientific discovery. A query language that supports biological science must be capable of expressing and implementing biological investigations. The biological query language (BQL) presented in this paper aims to enhance the scientists querying ability by: (1) providing an intermediate query language between scientific workflows and traditional query languages such as SQL, (2) expressing operators such as ranking and validating, not made directly available by traditional query languages and often difficult to express (by complex queries), and (3) constraining the evaluation of their operators by various semantics. This paper shows step by step how the overall problem of identifying genes related to a disease may be translated into a succession of BQL queries.

关键词： Database languages bioinformatics

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