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

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Using parallel algorithms for searching molecular sequence databases 利用并行算法搜索分子序列数据库
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.139
C.C.T. dos Reis, R. Mondaini
{"title":"Using parallel algorithms for searching molecular sequence databases","authors":"C.C.T. dos Reis, R. Mondaini","doi":"10.1109/CSBW.2005.139","DOIUrl":"https://doi.org/10.1109/CSBW.2005.139","url":null,"abstract":"This work presents the development of algorithms for approximate string matching using parallel methods. It intends to do the maximum of molecular sequences comparisons per unity of time. The parallel program implementation has carried out in C on an available twenty processing nodes clustering architecture using a model of parallel programming systems, the MPI (Message-Passing Interface), which is as library of subroutines. We use one of the possible approaches to reduce the time spent on comparisons of molecular database sequences by distributing the data among processors, which achieves a linear speedup (time) and requires constant space memory per processor.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"41 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":"116200927","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
ssahaSNP - a polymorphism detection tool on a whole genome scale ssahaSNP -全基因组多态性检测工具
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.128
Z. Ning, M. Cáccamo, J. Mullikin
{"title":"ssahaSNP - a polymorphism detection tool on a whole genome scale","authors":"Z. Ning, M. Cáccamo, J. Mullikin","doi":"10.1109/CSBW.2005.128","DOIUrl":"https://doi.org/10.1109/CSBW.2005.128","url":null,"abstract":"We present a software package which can detect homozygous SNPs and indels on a eukaryotic genome scale from millions of shotgun reads. Matching seeds of a few kmer words are found to locate the position of the read on the genome. Full sequence alignment is performed to detect base variations. Quality values of both variation bases and neighbouring bases are checked to exclude possible sequence base errors. To analyze polymorphism level in the genome, we used the package to detect indels from 20 million WGS reads against the draft WGS assembly. From the dataset, we detected a total number of 663,660 indels, giving an estimated average indel density at about one indel every 2.48 kilobases. Distribution of indels length and variation of indel mapped times are also analyzed.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"46 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":"116276522","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
Maximum significance clustering of oligonucleotide microarrays 寡核苷酸微阵列的最大显著聚类
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.91
D. Ridder, M. Reinders, F. Staal, J. Dongen
{"title":"Maximum significance clustering of oligonucleotide microarrays","authors":"D. Ridder, M. Reinders, F. Staal, J. Dongen","doi":"10.1109/CSBW.2005.91","DOIUrl":"https://doi.org/10.1109/CSBW.2005.91","url":null,"abstract":"Affymetrix high-density oligonucleotide microarrays measure expression of DNA transcripts using probe sets, i.e. multiple probes per transcript. Usually, these multiple measurements are transformed into a single probeset expression level before data analysis proceeds; any information on variability is lost. In this work we demonstrate how individual probe measurements can be used in a statistic for differential expression. Furthermore, we show how this statistic can serve as a clustering criterion. A novel clustering algorithm using this maximum significance criterion is demonstrated to be more efficient with the measured data than competing techniques for dealing with repeated measurements, especially when the sample size is small.","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":"129563369","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
Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM 扩展了3D-EM柔性装配过程中超族结构信息的引入
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.65
J. Velázquez-Muriel, J. Carazo
{"title":"Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM","authors":"J. Velázquez-Muriel, J. Carazo","doi":"10.1109/CSBW.2005.65","DOIUrl":"https://doi.org/10.1109/CSBW.2005.65","url":null,"abstract":"A new procedure to increase the number of aminoacids that are taken into account in the structural alignment core when performing flexible fitting with superfamily information in three-dimensional electron microscopy (3D-EM) is described. We propose to use incremental singular value decomposition (ISVD) instead of regular SVD to compute the principal components of the alignment core, in this way allowing to add new data and to estimate missing values. The results proof that positions of the alignment with gaps contain variational information that improves the models built for the fitting step of the procedure.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"73 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":"127402057","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
MassTRAQ: a fully automated tool for iTRAQ-labeled protein quantification MassTRAQ: itraq标记蛋白定量的全自动工具
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.89
Wen-Ting Lin, K. Wu, Wei-Neng Hung, Yi-Hwa Yian, Yet-Ran Chen, Yu-Ju Chen, Ting-Yi Sung, W. Hsu
{"title":"MassTRAQ: a fully automated tool for iTRAQ-labeled protein quantification","authors":"Wen-Ting Lin, K. Wu, Wei-Neng Hung, Yi-Hwa Yian, Yet-Ran Chen, Yu-Ju Chen, Ting-Yi Sung, W. Hsu","doi":"10.1109/CSBW.2005.89","DOIUrl":"https://doi.org/10.1109/CSBW.2005.89","url":null,"abstract":"Mass spectrometry has emerged to be one of the most powerful high throughput techniques for protein analysis, and iTRAQ labeling technique is the one of the newest techniques for protein identification and quantification in this field. Here, we display a new protein abundance analysis software for iTRAQ technique called MassTRAQ that can analyze up to four sets of samples at the same time. We have analyzed two samples with expression level 1:1, and have the result of 1:1.007 with standard deviation 0.004. Thus, MassTRAQ provides a good interpretation of the protein analysis.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"73 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":"127239299","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: 7
SinicView: an interactive visualization tool for comparison of multiple sequence alignment results SinicView:用于比较多个序列比对结果的交互式可视化工具
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.127
A. C. Shih, D. T. Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Chun-Yi Wong, M. Chou, T. Shiao
{"title":"SinicView: an interactive visualization tool for comparison of multiple sequence alignment results","authors":"A. C. Shih, D. T. Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Chun-Yi Wong, M. Chou, T. Shiao","doi":"10.1109/CSBW.2005.127","DOIUrl":"https://doi.org/10.1109/CSBW.2005.127","url":null,"abstract":"In the initial stage of sequence analysis, a biologist is first faced with the questions about how to choose the best tool to align sequences of interest and how to analyze and visualize the alignment results, and then with the question about whether unaligned regions produced by the tool are indeed not homologous or are just results due to inappropriate alignment tools or scoring systems used. In this paper, we present a versatile alignment visualization system, called SinicView, (for sequence-aligning innovative and interactive comparison viewer), which allows users to efficiently compare and evaluate assorted alignment results obtained by different tools. SinicView calculates similarity of the alignment outputs under a sliding window using the sum-of-pairs method and provides scoring profiles of each set of aligned sequences. Combined with the annotations information, the user can visually compare alignment results either in graphic scoring profiles or in plain text format of the aligned nucleotides. With SinicView. users can use their own data sequences to compare various alignment tools or scoring systems and select the most suitable one to perform alignment and sequence analysis. SinicView is avaiable for free download from http://biocomp.iis.sinica.edu/.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"80 2 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":"130720140","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
A diffusion model to estimate the inter-arrival time of charged molecules in stochastic event based modeling of complex biological networks 基于随机事件的复杂生物网络建模中估计带电分子到达时间的扩散模型
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.6
P. Ghosh, Samik Ghosh, K. Basu, Sajal K. Das
{"title":"A diffusion model to estimate the inter-arrival time of charged molecules in stochastic event based modeling of complex biological networks","authors":"P. Ghosh, Samik Ghosh, K. Basu, Sajal K. Das","doi":"10.1109/CSBW.2005.6","DOIUrl":"https://doi.org/10.1109/CSBW.2005.6","url":null,"abstract":"With biological experiments generating lots of empirical data, the challenge is to develop a modeling paradigm that integrates structural, molecular and genetic data for a quantitative understanding of physiology and behavior of biological processes at multiple scales - starting from cell, to tissues and finally to the whole organism. The complexity of the problem motivates the use of computer or \"in silico\" stochastic event based modeling approach. We focus on the signal transduction cascade triggered by extra-cellular Mg/sup 2+/ concentration in the two component PhoPQ regulatory system of Salmonella Enterica serovar Thphimurium, and present the mathematical formulation for the estimation of statistical parameters of inter-arrival time of molecules/ions to a cell receptor as external signal.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"80 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":"130854173","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: 8
HIV structural and biothermodynamics databases: a resource for the pharmaceutical and biotechnology industry 艾滋病毒结构和生物热力学数据库:制药和生物技术行业的资源
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.71
T. Bhat, Y. B. Tewari, H. Rodriguez, R. Goldberg
{"title":"HIV structural and biothermodynamics databases: a resource for the pharmaceutical and biotechnology industry","authors":"T. Bhat, Y. B. Tewari, H. Rodriguez, R. Goldberg","doi":"10.1109/CSBW.2005.71","DOIUrl":"https://doi.org/10.1109/CSBW.2005.71","url":null,"abstract":"Federal agencies, academia and industries have invested heavily in the development of structural and biothermodynamic data. However, the data are still largely distributed over several public and private archives leading to issues of inadequate interoperability. In order to maximize the investment made in these areas it is necessary to make it widely available to, and easily accessible to continued development and use by a broad community of researchers and industrialists. For this reason, during the last several years we have been working on developing and maintaining two databases; an integrated structural data resource for AIDS (http://xpdh.nist.gov/hivsdb/hivsdb.html) and a biothermodynamic data resource (http://xpdh.nist.gov/enzyme/spl I.bar/thermodynamics ).","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"40 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":"115645532","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
Chemical structure-activity relationship visualization using structure-activity maps 利用构效图可视化化学构效关系
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.34
Weiguo Fan, Xin Lin, Y. Hsieh, J. Baker, Boren Lin, Chun-che Tsai
{"title":"Chemical structure-activity relationship visualization using structure-activity maps","authors":"Weiguo Fan, Xin Lin, Y. Hsieh, J. Baker, Boren Lin, Chun-che Tsai","doi":"10.1109/CSBW.2005.34","DOIUrl":"https://doi.org/10.1109/CSBW.2005.34","url":null,"abstract":"This study shows an effective way to explore and visualize the structure-activity relationships (SARs) of flavonoids with antioxidant activity using structure- activity maps (SAMs). SAMs are graphical maps plotting molecular descriptors such as NAB or MSI against their biological activities. NAB (number of non-hydrogen atoms and bonds in a molecule) or MSI (molecular similarity index) is used to quantify the chemical structures. SA Ms pro vide a very efficient method for representing and visualizing SAR information in a biochemical database. SAMs also provide a simple and effective way for ordering and grouping compounds. SA Ms were examined for compounds grouped according to NAB to determine important activity trends utilizing structural orderings. SA Ms were used to systematically identify the effects of chemical modification on the activities of compounds and to determine the site and type of modifications for improved activity.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"42 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":"123869208","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
Considerations in making microarray cross-platform correlations 制作微阵列跨平台相关性的注意事项
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.44
M. Kollegal, S. Adak, R. Shippy, T. Sendera
{"title":"Considerations in making microarray cross-platform correlations","authors":"M. Kollegal, S. Adak, R. Shippy, T. Sendera","doi":"10.1109/CSBW.2005.44","DOIUrl":"https://doi.org/10.1109/CSBW.2005.44","url":null,"abstract":"Comparison and integration of expression data derived from diverse microarray platforms is challenging. Factors affecting cross-platform comparison of microarray data include the choice of normalization method used, annotation differences, presence of splice variants, RNA degradation and probe distance from 3' end. A thorough evaluation of two commercial microarray platforms to determine an appropriate methodology for making cross-platform correlations is described here.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"49 2 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":"124977120","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
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