Proceedings. International Conference on Intelligent Systems for Molecular Biology最新文献_第3页

A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. 一个新的快速启发式计算断点系统发育和实验系统发育分析的真实和合成数据。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

M E Cosner, R K Jansen, B M Moret, L A Raubeson, L S Wang, T Warnow, S Wyman

{"title":"A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data.","authors":"M E Cosner, R K Jansen, B M Moret, L A Raubeson, L S Wang, T Warnow, S Wyman","doi":"","DOIUrl":"","url":null,"abstract":"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.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21812143","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

Genes, themes and microarrays: using information retrieval for large-scale gene analysis. 基因、主题和微阵列:利用信息检索进行大规模基因分析。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

H Shatkay, S Edwards, W J Wilbur, M Boguski

引用次数: 0

Mining for putative regulatory elements in the yeast genome using gene expression data. 利用基因表达数据挖掘酵母基因组中可能的调控元件。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

J Vilo, A Brazma, I Jonassen, A Robinson, E Ukkonen

{"title":"Mining for putative regulatory elements in the yeast genome using gene expression data.","authors":"J Vilo, A Brazma, I Jonassen, A Robinson, E Ukkonen","doi":"","DOIUrl":"","url":null,"abstract":"We have developed a set of methods and tools for automatic discovery of putative regulatory signals in genome sequences. The analysis pipeline consists of gene expression data clustering, sequence pattern discovery from upstream sequences of genes, a control experiment for pattern significance threshold limit detection, selection of interesting patterns, grouping of these patterns, representing the pattern groups in a concise form and evaluating the discovered putative signals against existing databases of regulatory signals. The pattern discovery is computationally the most expensive and crucial step. Our tool performs a rapid exhaustive search for a priori unknown statistically significant sequence patterns of unrestricted length. The statistical significance is determined for a set of sequences in each cluster with respect to a set of background sequences allowing the detection of subtle regulatory signals specific for each cluster. The potentially large number of significant patterns is reduced to a small number of groups by clustering them by mutual similarity. Automatically derived consensus patterns of these groups represent the results in a comprehensive way for a human investigator. We have performed a systematic analysis for the yeast Saccharomyces cerevisiae. We created a large number of independent clusterings of expression data simultaneously assessing the \"goodness\" of each cluster. For each of the over 52,000 clusters acquired in this way we discovered significant patterns in the upstream sequences of respective genes. We selected nearly 1,500 significant patterns by formal criteria and matched them against the experimentally mapped transcription factor binding sites in the SCPD database. We clustered the 1,500 patterns to 62 groups for which we derived automatically alignments and consensus patterns. Of these 62 groups 48 had patterns that have matching sites in SCPD database.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21813098","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

Towards a systematics for protein subcelluar location: quantitative description of protein localization patterns and automated analysis of fluorescence microscope images. 迈向蛋白质亚细胞定位的分类学:蛋白质定位模式的定量描述和荧光显微镜图像的自动分析。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

R F Murphy, M V Boland, M Velliste

{"title":"Towards a systematics for protein subcelluar location: quantitative description of protein localization patterns and automated analysis of fluorescence microscope images.","authors":"R F Murphy, M V Boland, M Velliste","doi":"","DOIUrl":"","url":null,"abstract":"Determination of the functions of all expressed proteins represents one of the major upcoming challenges in computational molecular biology. Since subcellular location plays a crucial role in protein function, the availability of systems that can predict location from sequence or high-throughput systems that determine location experimentally will be essential to the full characterization of expressed proteins. The development of prediction systems is currently hindered by an absence of training data that adequately captures the complexity of protein localization patterns. What is needed is a systematics for the subcellular locations of proteins. This paper describes an approach to the quantitative description of protein localization patterns using numerical features and the use of these features to develop classifiers that can recognize all major subcellular structures in fluorescence microscope images. Such classifiers provide a valuable tool for experiments aimed at determining the subcellular distributions of all expressed proteins. The features also have application in automated interpretation of imaging experiments, such as the selection of representative images or the rigorous statistical comparison of protein distributions under different experimental conditions. A key conclusion is that, at least in certain cases, these automated approaches are better able to distinguish similar protein localization patterns than human observers.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21811351","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

Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold. 午夜区的微光:序列不同的蛋白质中排列相同残基的特征，它们共享一个共同的折叠。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

I Friedberg, T Kaplan, H Margalit

{"title":"Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold.","authors":"I Friedberg, T Kaplan, H Margalit","doi":"","DOIUrl":"","url":null,"abstract":"Sequence comparison of proteins that adopt the same fold has revealed a large degree of sequence variation. There are many pairs of structurally similar proteins with only a very low percentage of identical residues at structurally aligned positions. It is not clear whether these few identical residues have been conserved just by coincidence, or due to their structural and/or functional role The current study focuses on characterization of STructurally Aligned Identical ResidueS (STAIRS) in a data set of protein pairs that are structurally similar but sequentially dissimilar. The conservation pattern of the residues at structurally aligned positions has been characterized within the protein families of the two pair members, and mutually highly and weakly conserved positions of STAIRS could be identified About 40% of the STAIRS are only moderately conserved, suggesting that their maintenance may have been coincidental. The mutually highly conserved STAIRS show distinct features that are associated with protein structure and function: a relatively high fraction of these STAIRS are buried within their protein structures. Glycine, cysteine, histidine, and tryptophan are significantly over-represented among the mutually conserved STAIRS. A detailed survey of these STAIRS reveals residue-specific roles in the determination of the protein's structure and function.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21812149","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

An exact algorithm to identify motifs in orthologous sequences from multiple species. 一个精确的算法，以识别基序在同源序列从多个物种。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

M Blanchette, B Schwikowski, M Tompa

引用次数: 0

Robust parametric and semi-parametric spot fitting for spot array images. 点阵图像的鲁棒参数和半参数点拟合。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

N Brändle, H Y Chen, H Bischof, H Lapp

引用次数: 0

An evaluation of ontology exchange languages for bioinformatics. 生物信息学本体交换语言评价。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

R McEntire, P Karp, N Abernethy, D Benton, G Helt, M DeJongh, R Kent, A Kosky, S Lewis, D Hodnett, E Neumann, F Olken, D Pathak, P Tarczy-Hornoch, L Toldo, T Topaloglou

{"title":"An evaluation of ontology exchange languages for bioinformatics.","authors":"R McEntire, P Karp, N Abernethy, D Benton, G Helt, M DeJongh, R Kent, A Kosky, S Lewis, D Hodnett, E Neumann, F Olken, D Pathak, P Tarczy-Hornoch, L Toldo, T Topaloglou","doi":"","DOIUrl":"","url":null,"abstract":"Ontologies are specifications of the concepts in a given field, and of the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they satisfied each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received the highest scores: OML and Ontolingua. The result of those experiments, and the main conclusion of this study, was that the frame-based semantic model of Ontolingua is preferable to the conceptual graph model of OML, but that the XML-based syntax of OML is preferable to the Lisp-based syntax of Ontolingua.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21811350","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

Biclustering of expression data. 表达式数据的双聚类。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

Y Cheng, G M Church

引用次数: 0

Reducing mass degeneracy in SAR by MS by stable isotopic labeling. 稳定同位素标记的质谱法还原SAR中的质量简并。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 2000-01-01

C Bailey-Kellogg, J J Kelley, C Stein, B R Donald

{"title":"Reducing mass degeneracy in SAR by MS by stable isotopic labeling.","authors":"C Bailey-Kellogg, J J Kelley, C Stein, B R Donald","doi":"","DOIUrl":"","url":null,"abstract":"Mass spectrometry (MS) promises to be an invaluable tool for functional genomics, by supporting low-cost, high-throughput experiments. However, large-scale MS faces the potential problem of mass degeneracy--indistinguishable masses for multiple biopolymer fragments (e.g. from a limited proteolytic digest). This paper studies the tasks of planning and interpreting MS experiments that use selective isotopic labeling, thereby substantially reducing potential mass degeneracy. Our algorithms support an experimental-computational protocol called Structure-Activity Relation by Mass Spectrometry (SAR by MS), for elucidating the function of protein-DNA and protein-protein complexes. SAR by MS enzymatically cleaves a crosslinked complex and analyzes the resulting mass spectrum for mass peaks of hypothesized fragments. Depending on binding mode, some cleavage sites will be shielded; the absence of anticipated peaks implicates corresponding fragments as either part of the interaction region or inaccessible due to conformational change upon binding. Thus different mass spectra provide evidence for different structure-activity relations. We address combinatorial and algorithmic questions in the areas of data analysis (constraining binding mode based on mass signature) and experiment planning (determining an isotopic labeling strategy to reduce mass degeneracy and aid data analysis). We explore the computational complexity of these problems, obtaining upper and lower bounds. We report experimental results from implementations of our algorithms.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21812193","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