2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)最新文献_第4页

Improving operon prediction in E. coli 改进大肠杆菌操作子预测

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.76

P. Dam, V. Olman, Ying Xu

{"title":"Improving operon prediction in E. coli","authors":"P. Dam, V. Olman, Ying Xu","doi":"10.1109/CSBW.2005.76","DOIUrl":"https://doi.org/10.1109/CSBW.2005.76","url":null,"abstract":"In bacterium, genes working in the same pathway or interacting with each other are often organized into operons. Currently, the prediction accuracy for operon/boundary gene pairs is fairly good in Escherichia coli, however, such a high level of success in recognizing a gene pair as a boundary or operon pair does not automatically transcribe into a high level of accuracy in predicting the boundary of operons. We found that for several operon prediction programs, the prediction accuracy is often less accurate when the intergenic region of a gene pair is between 40 to 250 base pairs. In our approach, multiple features of the intergenic region, gene length and available microarray data in E. coli were used to improve the accuracy of the operon prediction programs in general and of gene pairs in the above intergenic region in particular. These features were scored according to a log likelihood formula, and the result suggests that we can gain up to 8% increase in the accuracy level for gene pairs with the intergenic distance between 40-250 base pairs. For other regions, the newly added features also give a moderate improvement in prediction accuracy. Furthermore, the accuracy in predicting transcript boundary is also improved, comparing to methods using the intergenic distance and functional annotation alone. We are currently fine-tuning our program to predict all operons in E. coli, and applying this method to predict operons in other organisms.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131243215","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: 2

Joint genomic and metabolomic analysis of toxic dose-response experiments 毒性剂量反应实验的联合基因组学和代谢组学分析

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.81

G. Jahns, N. DelRaso, Mark P. Westrick, Victor Chan, N. Reo, T. Zacharewski

引用次数: 0

An approach to generating and verifying complex scripts and procedures 生成和验证复杂脚本和过程的方法

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.21

J. Rash, M. Hinchey, D. Gračanin

{"title":"An approach to generating and verifying complex scripts and procedures","authors":"J. Rash, M. Hinchey, D. Gračanin","doi":"10.1109/CSBW.2005.21","DOIUrl":"https://doi.org/10.1109/CSBW.2005.21","url":null,"abstract":"Currently available tools and methods for system development that start with a formal model of a system and mechanically produce a provably equivalent implementation are valuable but not sufficient. The \"gap\" that such tools and methods leave unfilled is that the formal models cannot be proven to be equivalent to the system requirements as originated by the customer. For the classes of complex systems whose behavior can be described as a finite (but significant) set of scenarios, we offer a method for mechanically transforming requirements expressed in restricted natural language, or appropriate graphical notations, into a provably equivalent formal model that can be used as the basis for code generation and other transformations. The same approach may be applied to address computer science aspects of bioinformatics problems. Many software tools for bioinformatics have been developed using scripting languages such as Perl and Python. Scripts are developed based on a set of requirements that can be expressed using English-like statements. Using our approach, these may be used to automatically generate and validate scripts rather than write them from scratch.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"94 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115969963","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: 3

Identifying orthologs: cycle splitting on the breakpoint graph 识别同源物:断点图上的循环分裂

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.73

K. M. Swenson, N. Pattengale, Bernard M. E. Moret

引用次数: 0

Aligning peaks across multiple mass spectrometry data sets using a scale-space based approach 使用基于尺度空间的方法对齐多个质谱数据集的峰

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.19

Weichuan Yu, Xiaoye Li, Hongyu Zhao

引用次数: 1

Protein secondary structure prediction using support vector machine with a PSSM profile and an advanced tertiary classifier 基于PSSM和高级三级分类器的支持向量机蛋白质二级结构预测

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.114

Hae-Jin Hu, P. Tai, R. Harrison, Jieyue He, Yi Pan

引用次数: 3

A fast shotgun assembly heuristic 快速霰弹枪组装启发式

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.7

C. Wilks, S. Khuri

引用次数: 5

Efficient sampling of protein folding pathways using HMMSTR and probabilistic roadmaps 利用HMMSTR和概率路线图对蛋白质折叠途径进行有效采样

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.59

Y. Girdhar, C. Bystroff, Srinivas Akella

引用次数: 1

Mapping SNP association results into type 2 DM pathways-metabolic syndrome as a robust system 映射SNP关联导致2型糖尿病途径-代谢综合征作为一个强大的系统

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.87

T. Kido, Masanori Baba, Guijin Ji, Hidenori Satoh, Masaaki Muramatsu

引用次数: 0

Inverse design of large molecules using linear diophantine equations 利用线性丢番图方程的大分子反设计

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.79

Shawn Martin, W. M. Brown, J. Faulon, Derick C. Weis, D. Visco

{"title":"Inverse design of large molecules using linear diophantine equations","authors":"Shawn Martin, W. M. Brown, J. Faulon, Derick C. Weis, D. Visco","doi":"10.1109/CSBW.2005.79","DOIUrl":"https://doi.org/10.1109/CSBW.2005.79","url":null,"abstract":"We have previously developed a method for the inverse design of small ligands. This method can be used to design novel compounds with optimized properties (such as drugs) and has been applied successfully to the design of small peptide antagonists to leukocyte functional antigen-1 (LFA-1) and its intercellular adhesion molecule (ICAM-1). A key step in our method involves computing the Hilbert basis of a system of linear Diophantine equations. In our previous application, the ligands considered were small peptide rings, so that the resulting system of Diophantine equations was relatively small and easy to solve. When considering larger molecules, however, the Diophantine system is larger and more difficult to solve. In this work we present a method for reducing the system of Diophantine equations before they are solved, allowing the inverse design of larger compounds. We present this reduction on our original LFA-1/ICAM-1 dataset, where we were able to reduce a system with 24 equations and 49 variables to an equivalent system with 11 equations and 34 variables, giving a 10 times speedup in performance. We also present the results of our reduction on two new datasets, neither of which we could solve previously: a set of 27 conazole fungicides and a set of 61 /spl gamma/-secrerase inhibitors.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132506379","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: 1