Proceedings. IEEE Computer Society Bioinformatics Conference最新文献_第8页

Accelerating approximate subsequence search on large protein sequence databases 加速大型蛋白质序列数据库的近似子序列搜索

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039343

Jiong Yang, Wei Wang, Yi Xia, Philip S. Yu

引用次数: 7

HIV protease structural database HIV蛋白酶结构数据库

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039363

V. Ravichandran, J. Vondrášek, G. Gilliland, T. Bhat, A. Wlodawer

引用次数: 0

Towards automatic clustering of protein sequences 蛋白质序列的自动聚类

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039340

Jiong Yang, Wei Wang

{"title":"Towards automatic clustering of protein sequences","authors":"Jiong Yang, Wei Wang","doi":"10.1109/CSB.2002.1039340","DOIUrl":"https://doi.org/10.1109/CSB.2002.1039340","url":null,"abstract":"Analyzing protein sequence data becomes increasingly important recently. Most previous work on this area has mainly focused on building classification models. In this paper we investigate in the problem of automatic clustering of unlabeled protein sequences. As a widely recognized technique in statistics and computer science, clustering has been proven very useful in detecting unknown object categories and revealing hidden correlations among objects. One difficulty, that prevents clustering from being performed directly on protein sequence is the lack of an effective similarity measure that can be computed efficiently. Therefore, we propose a novel model for protein sequence cluster by exploring significant statistical properties possessed by the sequences. The concept of imprecise probabilities are introduced to the original probabilistic suffix tree to monitor the convergence of the empirical measurement and to guide the clustering process. It is demonstrated that the proposed method can successfully discover meaningful families without the necessity of learning models of different families from pre-labeled \"training data\".","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"1 1","pages":"175-186"},"PeriodicalIF":0.0,"publicationDate":"2002-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/CSB.2002.1039340","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62214278","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: 17

Complexity and application of pedigree analysis programme GTree 谱系分析程序GTree的复杂性及其应用

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039358

D. Ogino, S. Mori, M. Nose, Hideki Sawada

引用次数: 3

A reference database for Medicago truncatula genes, proteins, and metabolites 短叶苜蓿基因、蛋白和代谢产物的参考数据库

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039366

D. Guo, Xingjing Li, A. Kamal, O. Brazhnik, P. Mendes

引用次数: 0

DNA sequence compression using the Burrows-Wheeler Transform 利用Burrows-Wheeler变换的DNA序列压缩

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039352

D. Adjeroh, Yong Zhang, A. Mukherjee, M. Powell, T. Bell

引用次数: 59

Visualization techniques for genomic data 基因组数据可视化技术

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039354

A. Loraine, G. Helt

引用次数: 3

Rapid large-scale oligonucleotide selection for microarrays 微阵列快速大规模寡核苷酸选择

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039329

S. Rahmann

引用次数: 57

An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks 一种高效的蛋白质骨架核磁共振波峰分配分支结合算法

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039339

Guohui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, Jianjun Wen, Ying Xu

{"title":"An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks","authors":"Guohui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, Jianjun Wen, Ying Xu","doi":"10.1109/CSB.2002.1039339","DOIUrl":"https://doi.org/10.1109/CSB.2002.1039339","url":null,"abstract":"NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on our recent work towards automating the assignment process, particularly the process of backbone resonance peak assignment. We formulate the assignment problem as a constrained weighted bipartite matching problem. While the problem, in the most general situation, is NP-hard, we present an efficient solution based on a branch-and-bound algorithm with effective bounding techniques and a greedy filtering algorithm for reducing the search space. Our experimental results on 70 instances of (pseudo) real NMR data derived from 14 proteins demonstrate that the new solution runs much faster than a recently introduced (exhaustive) two-layer algorithm and recovers more correct peak assignments than the two-layer algorithm.","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"1 1","pages":"165-174"},"PeriodicalIF":0.0,"publicationDate":"2002-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/CSB.2002.1039339","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62214271","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: 22

A bi-recursive neural network architecture for the prediction of protein coarse contact maps 一种用于蛋白质粗接触图预测的双递归神经网络结构

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039341

A. Vullo, P. Frasconi

引用次数: 8