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检索条件"任意字段=IEEE Computational Systems Bioinformatics Conference"

共 879 条记录，以下是821-830 订阅

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A block coding method that leads to significantly lower entropy values for the proteins and coding sections of Haemophilus influenzae

A block coding method that leads to significantly lower entr...

引用

ieee conference on bioinformatics

作者： G. Sampath Department of Computer Science College of New Jersey Ewing NJ USA

A simple statistical block code in combination with the LZW-based compression utilities gzip and compress has been found to increase by a significant amount the level of compression possible for the proteins encoded in Haemophilus influenzae, the first fully sequenced genome. The method yields an entropy value of 3.665 bits per symbol (bps), which is 0.657 bps below the maximum of 4.322 bps and an improvement of 0.452 bps over the best known to date of 4.118 bps using Matsumoto, Sadakane, and Imai's Iza-CTW algorithm. Calculations based on a compact inverse genetic code show that the genome has a maximum entropy of 1.757 bps for the coding regions, with a possibly lower actual entropy. These results hint at the existence of hitherto unexplored redundancies that do not show up in Markov models and are indicative of more internal structure than suspected in both the protein and the genome.

关键词： Block codes Entropy Proteins bioinformatics Biological information theory Genomics Distributed computing Biology computing Data mining Chemicals

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Fast and accurate probe selection algorithm for large genomes

Fast and accurate probe selection algorithm for large genome...

引用

ieee conference on bioinformatics

作者： W.-K. Sung W.-H. Lee Department of Computer Science National University of Singapore Singapore Genome Institute of Singapore Singapore

The oligo microarray (DNA chip) technology in recent years has a significant impact on genomic study. Many fields such as gene discovery, drug discovery, toxicological research and disease diagnosis, will certainly benefit from its use. A microarray is an orderly arrangement of thousands of DNA fragments where each DNA fragment is a probe (or a fingerprint) of a gene/cDNA. It is important that each probe must uniquely associate with a particular gene/cDNA. Otherwise, the performance of the microarray will be affected. Existing algorithms usually select probes using the criteria of homogeneity, sensitivity, and specificity. Moreover, they improve efficiency employing some heuristics. Such approaches reduce the accuracy. Instead, we make use of some smart filtering techniques to avoid redundant computation while maintaining the accuracy. Based on the new algorithm, optimal short (20 bases) or long (50 or 70 bases) probes can be computed efficiently for large genomes.

关键词： Probes Genomics bioinformatics DNA Pharmaceutical technology Drugs Toxicology Diseases Fingerprint recognition Filtering

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Automatic recognition of regions of intrinsically poor multiple alignment using machine learning

Automatic recognition of regions of intrinsically poor multi...

引用

ieee conference on bioinformatics

作者： Y. Shan E.E. Milios A.J. Roger C. Blouin E. Susko Faculty of Computer Science Dalhousie University Halifax NS Canada Department of Biochemistry and Molecular Biology Genome Atlantic Genome Canada Dalhousie University Halifax NS Canada Department of Mathematics and Statistics Dalhousie University Halifax NS Canada

Phylogenetic analysis requires alignment of gene or protein sequences. Some regions of genes evolve fast and suffer numerous insertion and deletion events and cannot be aligned reliably with automatic alignment algorithms. Such regions of intrinsically uncertain alignment are currently detected and deleted manually before performing phylogenetic analysis. We present the results of a machine learning approach to detect regions of poor alignment automatically. We compare the results obtained from Naive Bayes (NB), C4.5 decision tree (C4.5) and support vector machine (SVM) approaches.

关键词： Machine learning Support vector machines Support vector machine classification Phylogeny bioinformatics Niobium Genomics Sequences Decision trees Training data

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Estimating recombination rate distribution by optimal quantization

Estimating recombination rate distribution by optimal quanti...

引用

ieee conference on bioinformatics

作者： M. Song S. Boissinot R.M. Haralick I.T. Phillips Department of Computer Science Queen's College Flushing NY USA Department of Biology Queen's College Flushing NY USA Doctoral Program in Computer Science Graduate CenterCity College and Graduate Center City University of New York New York NY USA

We obtain recombination rate distribution functions for all human chromosomes using an optimal quantization method. This nonparametric method allows us to control over-/under-fitting. The piece-wise constant recombination rate distribution functions are convenient to store and retrieve. Our experimental results showed more abrupt distribution functions than two recently published results. In the previous results, the over-/under-fitting issues were not addressed explicitly. Our estimation had greater log likelihood over a previous result using Parzen window. It suggests that the optimal quantization technique might be of great advantage for estimation of other genomic feature distributions.

关键词： Quantization Biological cells Distribution functions Humans Computer science Educational institutions bioinformatics Evolution (biology) Biology Genomics

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A computational approach to reconstructing gene regulatory networks

A computational approach to reconstructing gene regulatory n...

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ieee conference on bioinformatics

作者： X. Deng H. Ali Department of Computer Science College of Information Science and Technology University of Nebraska Omaha Omaha NE USA

With the rapid accumulation of gene expression data in publicly accessible databases, computational study of gene regulation has become an obtainable goal Intrinsic to this task will be data mining tools for inferring knowledge from biological data. In this project, we have developed a new data mining technique in which we adapt the connectivity of a recurrent neural network model by indexing regulatory elements and including nonlinear interaction terms. The new technique reduces the number of parameters by O(n), therefore increasing the chance of recovering the underlying regulatory network. In order to fit the model from data, we have developed a genetic fitting algorithm with O(n) time complexity and that adapts the connectivity during the fitting process until a satisfactory fit is obtained. We have implemented this fitting algorithm and applied it to two data sets: rat central nervous system development (CNS) data with 112 genes, and yeast whole genome data with 2467 genes. With multiple runs of the fitting algorithm, we were able to efficiently generate a statistical pattern of the model parameters from the data. Because of its adaptive features, this method will be especially useful for reconstructing coarse-grained gene regulatory network from large scale or genome scale gene expression data sets.

关键词： Computer networks Biology computing Gene expression Data mining Genomics bioinformatics Databases Recurrent neural networks Biological system modeling Indexing

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SMASHing regulatory sites in DNA by human-mouse sequence comparisons

SMASHing regulatory sites in DNA by human-mouse sequence com...

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ieee conference on bioinformatics

作者： M. Zavolan N. Rajewsky N.D. Socci T. Gaasterlamd Laboratory for Computational Genomics Rockefeller University NY USA Department of Biology New York University NY USA Physics and Biology Rockefeller University NY USA Department of Pathology Seaver Foundation for Bioinformatics Albert Einstein College of Medicine Bronx NY USA

Regulatory sequence elements provide important clues to understanding and predicting gene expression. Although the binding sites for hundreds of transcription factors are known, there has been no systematic attempt to incorporate this information in the annotation of the human genome. Cross species sequence comparisons are critical to a meaningful annotation of regulatory elements since they generally reside in conserved noncoding regions. To take advantage of the recently completed drafts of the mouse and human genomes for annotating transcription factor binding sites, we developed SMASH, a computational pipeline that identifies thousands of orthologous human/mouse proteins, maps them to genomic sequences, extracts and compares upstream regions and annotates putative regulatory elements in conserved, noncoding, upstream regions. Our current dataset consists of approximately 2500 human/mouse gene pairs. Transcription start sites were estimated by mapping quasifull length cDNA sequences. SMASH uses a novel probabilistic method to identify putative conserved binding sites that takes into account the competition between transcription factors for binding DNA. SMASH presents the results via a genome browser web interface which displays the predicted regulatory information together with the current annotations for the human genome. Our results are validated by comparison to previously published experimental data. SMASH results compare favorably to other existing computational approaches.

关键词： DNA Sequences Humans Genomics bioinformatics Mice Gene expression Pipelines Protein engineering Displays

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CoMRI: a compressed multiresolution index structure for sequence similarity queries

CoMRI: a compressed multiresolution index structure for sequ...

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ieee conference on bioinformatics

作者： H. Sun O. Ozturk H. Ferhatosmanoglu Department of Computer and Information Science Ohio State Uinversity USA Ohio State University Columbus OH US Dept. of Comput. & Inf. Sci. Ohio State Univ. Columbus OH USA

In this paper, we present CoMRI, compressed multiresolution index, our system for fast sequence similarity search in DNA sequence databases. We employ virtual bounding rectangle (VBR) concept to build a compressed, grid style index structure. An advantage of grid format over trees is subsequence location information is given by the order of corresponding VBR in the VBR list. Taking advantage of VBRs, our index structure fits into a reasonable size of memory easily. Together with a new optimized multiresolution search algorithm, the query speed is improved significantly. Extensive performance evaluations on human chromosome sequence data show that VBRs save 80%-93% index storage size compared to MBRs (minimum bounding rectangles) and new search algorithm prunes almost all unnecessary VBRs which guarantees efficient disk I/O and CPU cost. According to the results of our experiments, the performance of CoMRI is at least 100 times faster than MRS which is another grid index structure introduced very recently.

关键词： Sequences DNA Indexes bioinformatics Genomics Spatial databases Multidimensional systems Multiresolution analysis Sun Biomedical computing

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Haplotype pattern mining & classification for detecting disease associated site

Haplotype pattern mining & classification for detecting dise...

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ieee conference on bioinformatics

作者： T. Kido M. Baba H. Matsumine Y. Higashi H. Higuchi M. Muramatsu JowareHanzomon 2F HuBit Genomix Inc. Tokyo Japan NTT Data Company Limited Tokyo Japan School of Biomedical Science Tokyo Medical and Dental University Tokyo Japan

Finding the causative genes for common diseases using SNP (single nucleotide polymorphism) markers is now becoming a real challenge. Although traditional statistical SNP association tests exist, these tests could not explain the effects of SNP combinations or probable recombination histories from ancestral chromosomes. Haplotype analysis of disease associated site provides more powerful markers than individual SNP analysis, and can help identify probable causative mutations. In this paper, we introduce a new method for effective haplotype pattern mining to detect disease associated mutations. Using this procedure, we can discover some of the new disease associated SNPs, which can not be detected by traditional methods. We will introduce a powerful tool for implementing this procedure with some worked examples.

关键词： Diseases Genetic mutations Testing Phylogeny Tree graphs Frequency estimation Genomics bioinformatics Poles and towers Dentistry

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Aligning ESTs to genome using multilayer unique makers

Aligning ESTs to genome using multilayer unique makers

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ieee conference on bioinformatics

作者： F.R. Hsu J.F. Chen Department of Information Technology Taichung Healthcare and Management University Taiwan

As more and more genomic sequences have been sequenced and rapid growing of number of EST (expressed sequence tag), we need very fast and efficient algorithms to align ESTs to genome. ESTs contain the exon/intron structure. Let G and E denote the given genome and the given EST sequence respectively. In order to reduce the time complexity, it is quite important to locate the position of E in G efficiently. A unique maker is a sequence appeared in G only once. We can locate the position of E in G by finding unique markers contained in E. The time complexity to align ESTs to genome grows rapidly when we use longer unique markers. In this paper, we propose a multi-layer unique marker method to align ESTs to genome. Our method has the benefit of both short and long unique markers. Our algorithm can also use to locate the position of single nucleotide polymorphism (SNP). Experimental result shows that our method is much faster than common tools such as SIM4 and BLAT.

关键词： Genomics bioinformatics Sequences DNA Microcomputers Humans Information technology Medical services Technology management Proteins

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TC-DB: an architecture for membrane transport protein analysis

TC-DB: an architecture for membrane transport protein analys...

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ieee conference on bioinformatics

作者： C.V. Tran N.M. Yang M.H. Saier Division of Biological Sciences University of California at San Diego La Jolla CA USA

TC-DB is a comprehensive relational database containing structural, functional and evolutionary information about transmembrane transport proteins. The database contains factual material extracted from more than 9000 references, covering approximately 3000 representative proteins, classified into over 400 families. TC-DB is the primary resource allowing access to the data upon which the TC system is based. The TC system has been adopted by the international union of biochemistry and molecular biology (IUBMB). The functional ontology developed for TC-DB provides an infrastructure to develop powerful queries that yield biological insight. The TC-DB website offers a number of software tools that facilitate the analysis of membrane transporters. Multiple avenues of access are supported by the web interface including classification drill-down, parametric searching, and full-text searching. TC-DB has been used for the annotation of transport proteins in newly sequenced genomes and provides tools to trace evolutionary pathways. The database as well as web services are accessible free of charge at http://tcdb. ucsd. edu.

关键词： Biomembranes Proteins Relational databases Biological materials Data mining Biochemistry Ontologies Software tools Genomics bioinformatics

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