Proceedings. IEEE Computer Society Bioinformatics Conference最新文献_第3页

AntiClustal: Multiple Sequence Alignment by antipole clustering and linear approximate 1-median computation. 反簇:通过反极聚类和线性近似1-中位数计算的多序列比对。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

C Di Pietro, V Di Pietro, G Emmanuele, A Ferro, T Maugeri, E Modica, G Pigola, A Pulvirenti, M Purrello, M Ragusa, M Scalia, D Shasha, S Travali, V Zimmitti

{"title":"AntiClustal: Multiple Sequence Alignment by antipole clustering and linear approximate 1-median computation.","authors":"C Di Pietro, V Di Pietro, G Emmanuele, A Ferro, T Maugeri, E Modica, G Pigola, A Pulvirenti, M Purrello, M Ragusa, M Scalia, D Shasha, S Travali, V Zimmitti","doi":"","DOIUrl":"","url":null,"abstract":"In this paper we present a new Multiple Sequence Alignment (MSA) algorithm called AntiClusAl. The method makes use of the commonly use idea of aligning homologous sequences belonging to classes generated by some clustering algorithm, and then continue the alignment process ina bottom-up way along a suitable tree structure. The final result is then read at the root of the tree. Multiple sequence alignment in each cluster makes use of the progressive alignment with the 1-median (center) of the cluster. The 1-median of set S of sequences is the element of S which minimizes the average distance from any other sequence in S. Its exact computation requires quadratic time. The basic idea of our proposed algorithm is to make use of a simple and natural algorithmic technique based on randomized tournaments which has been successfully applied to large size search problems in general metric spaces. In particular a clustering algorithm called Antipole tree and an approximate linear 1-median computation are used. Our algorithm compared with Clustal W, a widely used tool to MSA, shows a better running time results with fully comparable alignment quality. A successful biological application showing high aminoacid conservation during evolution of Xenopus laevis SOD2 is also cited.","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"326-36"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25834134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Initial large-scale exploration of protein-protein interactions in human brain. 对人脑中蛋白质-蛋白质相互作用的初步大规模探索。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Jake Y Chen, Andrey Y Sivachenko, Russell Bell, Cornelia Kurschner, Irene Ota, Sudhir Sahasrabudhe

引用次数: 0

SMASHing regulatory sites in DNA by human-mouse sequence comparisons. 通过人鼠序列比较粉碎DNA中的调控位点。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Mihaela Zavolan, Nicholas D Socci, Nikolaus Rajewsky, Terry Gaasterlamd

{"title":"SMASHing regulatory sites in DNA by human-mouse sequence comparisons.","authors":"Mihaela Zavolan, Nicholas D Socci, Nikolaus Rajewsky, Terry Gaasterlamd","doi":"","DOIUrl":"","url":null,"abstract":"Regulatory sequence elements provide important clues to understanding and predicting gene expression. Although the binding sites for hundreds of transcription factors are known, there has been no systematic attempt to incorporate this information in the annotation of the human genome. Cross species sequence comparisons are critical to a meaningful annotation of regulatory elements since they generally reside in conserved non-coding regions. To take advantage of the recently completed drafts of the mouse and human genomes for annotating transcription factor binding sites, we developed SMASH, a computational pipeline that identifies thousands of orthologous human/ mouse proteins, maps them to genomic sequences, extracts and compares upstream regions and annotates putative regulatory elements in conserved, non-coding, upstream regions. Our current dataset consists of approximately 2,500 human/mouse gene pairs. Transcription start sites were estimated by mapping quasi-full length cDNA sequences. SMASH uses a novel probabilistic method to identify putative conserved binding sites that takes into account the competition between transcription factors for binding DNA. SMASH presents the results via a genome browser web interface which displays the predicted regulatory information together with the current annotations for the human genome. Our results are validated by comparison to previously published experimental data. SMASH results compare favorably to other existing computational approaches.","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"277-86"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25834890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computing highly specific and mismatch tolerant oligomers efficiently. 高效计算高特异性和错配容忍低聚物。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Tomoyuki Yamada, Shinichi Morishita

{"title":"Computing highly specific and mismatch tolerant oligomers efficiently.","authors":"Tomoyuki Yamada, Shinichi Morishita","doi":"","DOIUrl":"","url":null,"abstract":"The sequencing of the genomes of a variety of species and the growing databases containing expressed sequence tags (ESTs) and complementary DNAs (cDNAs) facilitate the design of highly specific oligomers for use as genomic markers, PCR primers, or DNA oligo microarrays. The first step in evaluating the specificity of short oligomers of about twenty units in length is to determine the frequencies at which the oligomers occur. However, for oligomers longer than about fifty units this is not efficient, as they usually have a frequency of only 1. A more suitable procedure is to consider the mismatch tolerance of an oligomer, that is, the minimum number of mismatches that allows a given oligomer to match a sub-sequence other than the target sequence anywhere in the genome or the EST database. However, calculating the exact value of mismatch tolerance is computationally costly and impractical. Therefore, we studied the problem of checking whether an oligomer meets the constraint that its mismatch tolerance is no less than a given threshold. Here, we present an efficient dynamic programming algorithm solution that utilizes suffix and height arrays. We demonstrated the effectiveness of this algorithm by efficiently computing a dense list of oligo-markers applicable to the human genome. Experimental results show that the algorithm runs faster than well-known Abrahamson's algorithm by orders of magnitude and is able to enumerate 63% to approximately 79% of qualified oligomers.","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"316-25"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25833646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Stochastic stage-structured modeling of the adaptive immune system. 适应性免疫系统的随机阶段结构模型。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Dennis L Chao, Miles P Davenport, Stephanie Forrest, Alan S Perelson

引用次数: 0

Stepping up the pace of discovery: the genomes to life program. 加快发现的步伐:基因组到生命的计划。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Marvin Frazier, David Thomassen, Aristides Patrinos, Gary Johnson, Carl E Oliver, Edward Uberbacher

{"title":"Stepping up the pace of discovery: the genomes to life program.","authors":"Marvin Frazier, David Thomassen, Aristides Patrinos, Gary Johnson, Carl E Oliver, Edward Uberbacher","doi":"","DOIUrl":"","url":null,"abstract":"Genome to life (GTL), the U.S Department of Energy Office of Science's systems biology program, focuses on environmental microbiology. Over the next 10 to 20 years, GTL's key goal is to understand the life processes of thousands of microbes and microbial systems in their native environments. This focus demands that we address huge gaps in knowledge, technology, computing, data capture and analysis, and systems-level integration. Distinguishing features include (1) strategies for unprecedented, comprehensive, and high-throughput data collection; (2) advanced computing, mathematics, algorithms, and data-management technologies; (3) a focus on potential microbial capabilities to help solve energy and environmental challenges; and (4) new research and management models that link production-scale systems biology facilities in an accessible environment. This unprecedented opportunity to provide the scientific foundation for solving urgent problems in energy, global climate change, and environmental cleanup demands that we take bold steps to achieve a much faster, more efficient pace of biological discovery.","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"2-9"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26133911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Efficient reconstruction of phylogenetic networks with constrained recombination. 基于约束重组的系统发育网络的高效重构。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Dan Gusfield, Satish Eddhu, Charles Langley

{"title":"Efficient reconstruction of phylogenetic networks with constrained recombination.","authors":"Dan Gusfield, Satish Eddhu, Charles Langley","doi":"","DOIUrl":"","url":null,"abstract":"A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not tree-like. 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.","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"363-74"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25834138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. 结合微阵列和生物知识估计基因网络通过贝叶斯网络。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano

引用次数: 0

Statistical and visual morph movie analysis of crystallographic mutant selection bias in protein mutation resource data. 蛋白质突变资源数据中晶体突变选择偏差的统计和视觉形态电影分析。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Werner G Krebs, Philip E Bourne

引用次数: 0

LOGOS: a modular Bayesian model for de novo motif detection. LOGOS:用于从头基序检测的模块化贝叶斯模型。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Eric P Xing, Wei Wu, Michael I Jordan, Richard M Karp

{"title":"LOGOS: a modular Bayesian model for de novo motif detection.","authors":"Eric P Xing, Wei Wu, Michael I Jordan, Richard M Karp","doi":"","DOIUrl":"","url":null,"abstract":"The complexity of the global organization and internal structures of motifs in higher eukaryotic organisms raises significant challenges for motif detection techniques. To achieve successful de novo motif detection it is necessary to model the complex dependencies within and among motifs and incorporate biological prior knowledge. In this paper, we present LOGOS, an integrated LOcal and GlObal motif Sequence model for biopolymer sequences, which provides a principled framework for developing, modularizing, extending and computing expressive motif models for complex biopolymer sequence analysis. LOGOS consists of two interacting submodels: HMDM, a local alignment model capturing biological prior knowledge and positional dependence within the motif local structure; and HMM, a global motif distribution model modeling frequencies and dependencies of motif occurrences. Model parameters can be fit using training motifs within an empirical Bayesian framework. A variational EM algorithm is developed for de novo motif detection. LOGOS improves over existing models that ignore biological priors and dependencies in motif structures and motif occurrences, and demonstrates superior performance on both semi-realistic test data and cis-regulatory sequences from yeast and Drosophila sequences with regard to sensitivity, specificity, flexibility and extensibility.","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"266-76"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25834889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0