Proceedings. International Conference on Intelligent Systems for Molecular Biology最新文献_第9页

The ribosome scanning model for translation initiation: implications for gene prediction and full-length cDNA detection. 翻译起始的核糖体扫描模型:基因预测和全长cDNA检测的意义。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

P Agarwal, V Bafna

{"title":"The ribosome scanning model for translation initiation: implications for gene prediction and full-length cDNA detection.","authors":"P Agarwal, V Bafna","doi":"","DOIUrl":"","url":null,"abstract":"Biological signals, such as the start of protein translation in eukaryotic mRNA, are stretches of nucleotides recognized by cellular machinery. There are a variety of techniques for modeling and identifying them. Most of these techniques either assume that the base pairs at each position of the signal are independently distributed, or they allow for limited dependencies among different positions. In previous work, we provided a statistical model that generalizes earlier methods and captures all significant high-order dependencies among different base positions. In this paper, we use a set of experimentally verified translation initiation (TI) sites (provided by Amos Bairoch) from eukaryotic sequences to train a range of methods, and then compare these methods. None of the methods is effective in predicting TI sites. We take advantage of the ribosome scanning model (Cigan et al., 1988) to significantly improve the prediction accuracy for full-length mRNAs. The ribosome scanning model suggests scanning from the 5' end of the capped mRNA and initiating translation at the first AUG in good context. This reduces the search space dramatically and accounts for its effectiveness. The success of this approach illustrates how biological ideas can illuminate and help solve challenging problems in computational biology.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20695510","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

The LabFlow system for workflow management in large scale biology research laboratories. LabFlow系统用于大型生物学研究实验室的工作流程管理。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

N Goodman, S Rozen, L D Stein

引用次数: 0

TAMBIS--Transparent Access to Multiple Bioinformatics Information Sources. TAMBIS—透明访问多个生物信息学信息源。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

P G Baker, A Brass, S Bechhofer, C Goble, N Paton, R Stevens

{"title":"TAMBIS--Transparent Access to Multiple Bioinformatics Information Sources.","authors":"P G Baker, A Brass, S Bechhofer, C Goble, N Paton, R Stevens","doi":"","DOIUrl":"","url":null,"abstract":"The TAMBIS project aims to provide transparent access to disparate biological databases and analysis tools, enabling users to utilize a wide range of resources with the minimum of effort. A prototype system has been developed that includes a knowledge base of biological terminology (the biological Concept Model), a model of the underlying data sources (the Source Model) and a 'knowledge-driven' user interface. Biological concepts are captured in the knowledge base using a description logic called GRAIL. The Concept Model provides the user with the concepts necessary to construct a wide range of multiple-source queries, and the user interface provides a flexible means of constructing and manipulating those queries. The Source Model provides a description of the underlying sources and mappings between terms used in the sources and terms in the biological Concept Model. The Concept Model and Source Model provide a level of indirection that shields the user from source details, providing a high level of source transparency. Source independent, declarative queries formed from terms in the Concept Model are transformed into a set of source dependent, executable procedures. Query formulation, translation and execution is demonstrated using a working example.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20695513","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

Phylogenetic inference in protein superfamilies: analysis of SH2 domains. 蛋白质超家族的系统发育推断:SH2结构域的分析。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

K Sjölander

引用次数: 0

Computational applications of DNA structural scales. DNA结构尺度的计算应用。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

P Baldi, Y Chauvin, S Brunak, J Gorodkin, A G Pedersen

引用次数: 0

A statistical theory of sequence alignment with gaps. 带间隙序列比对的统计理论。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

D Drasdo, T Hwa, M Lässig

引用次数: 0

GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome. GeneExpress:一种描述、分析和识别真核生物基因组调控序列的计算机系统。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

N A Kolchanov, M P Ponomarenko, A E Kel, Kondrakhin YuV, A S Frolov, F A Kolpakov, T N Goryachkovsky, O V Kel, E A Ananko, E V Ignatieva, O A Podkolodnaya, V N Babenko, I L Stepanenko, A G Romashchenko, T I Merkulova, D G Vorobiev, S V Lavryushev, Ponomarenko YuV, A V Kochetov, G B Kolesov, V V Solovyev, L Milanesi, N L Podkolodny, E Wingender, T Heinemeyer

{"title":"GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome.","authors":"N A Kolchanov, M P Ponomarenko, A E Kel, Kondrakhin YuV, A S Frolov, F A Kolpakov, T N Goryachkovsky, O V Kel, E A Ananko, E V Ignatieva, O A Podkolodnaya, V N Babenko, I L Stepanenko, A G Romashchenko, T I Merkulova, D G Vorobiev, S V Lavryushev, Ponomarenko YuV, A V Kochetov, G B Kolesov, V V Solovyev, L Milanesi, N L Podkolodny, E Wingender, T Heinemeyer","doi":"","DOIUrl":"","url":null,"abstract":"GeneExpress system has been designed to integrate description, analysis, and recognition of eukaryotic regulatory sequences. The system includes 5 basic units: (1) GeneNet contains an object-oriented database for accumulation of data on gene networks and signal transduction pathways and a Java-based viewer that allows an exploration and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor Binding Site Recognition contains a compilation of transcription factor binding sites (TFBSC) and programs for their analysis and recognition; (4) mRNA Translation is designed for analysis of structural and contextual features of mRNA 5'UTRs and prediction of their translation efficiency; and (5) ACTIVITY is the module for analysis and site activity prediction of a given nucleotide sequence. Integration of the databases in the GeneExpress is based on the Sequence Retrieval System (SRS) created in the European Bioinformatics Institute.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20696078","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

Segment-based scores for pairwise and multiple sequence alignments. 两两和多序列比对的基于片段的分数。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

B Morgenstern, W R Atchley, K Hahn, A Dress

引用次数: 0

A surface measure for probabilistic structural computations. 用于概率结构计算的表面度量。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

J P Schmidt, C C Chen, J L Cooper, R B Altman

{"title":"A surface measure for probabilistic structural computations.","authors":"J P Schmidt, C C Chen, J L Cooper, R B Altman","doi":"","DOIUrl":"","url":null,"abstract":"Computing three-dimensional structures from sparse experimental constraints requires method for combining heterogeneous sources of information, such as distances, angles, and measures of total volume, shape, and surface. For some types of information, such as distances between atoms, numerous methods are available for computing structures that satisfy the provided constraints. It is more difficult, however, to use information about the degree to which an atom is on the surface or buried as a useful constraint during structure computations. Surface measures have been used as accept/reject criteria for previously computed structures, but this is not an efficient strategy. In this paper, we investigate the efficacy of applying a surface measure in the computation of molecular structure, using a method of probabilistic least square computations which facilitates the introduction of multiple, noisy, heterogeneous data sources. For this purpose, we introduce a simple purely geometrical measure of surface proximity called maximal conic view (MCV). MCV is efficiently computable and differentiable, and is hence well suited to driving a structural optimization method based, in part, on surface data. As an initial validation, we show that MCV correlates well with known measures for total exposed surface area. We use this measure in our experiments to show that information about surface proximity (derived from theory or experiment, for example) can be added to a set of distance measurements to increase significantly the quality of the computed structure. In particular, when 30 to 50 percent of all possible short-range distances are provided, the addition of surface information improves the quality of the computed structure (as measured by RMS fit) by as much as 80 percent. Our results demonstrate that knowledge of which atoms are on the surface and which are buried can be used as a powerful constraint in estimating molecular structure.","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20696544","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

Identification of divergent functions in homologous proteins by induction over conserved modules. 同源蛋白在保守模组上的诱导鉴定。

Proceedings. International Conference on Intelligent Systems for Molecular Biology Pub Date : 1998-01-01

I Shah, L Hunter

引用次数: 0