biological sequence data analysis
Biological Sequence Clustering with Symbol Table Data Structure
... in biological sciences are: (1) CHAMELEON - used in measuring the similarity of clusters based on a dynamic model [31], (2) FOLDALIGNM - developed by Elfar Torarinsson et al [53] which makes use of multiple ...
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Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis
... different data structures, particularly suffix trees and suffix arrays, has been increasing steadily ...underlying sequence by efficiently supporting several look- up procedures ...index sequence, ...
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On avoided words, absent words, and their application to biological sequence analysis
... Algorithm AvoidedWords was implemented as a pro- gram to compute the ρ -avoided words of length k in one or more input sequences; there is an option to run Algorithm AllAvoidedWords instead. The program was imple- mented ...
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PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences
... transcriptome data from RNA-Seq experiments, solving the problem of mapping reads back to the host organism's genome [2] ...for analysis of most reads produced by the experiments, but these tools typically ...
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Analysis of Compression Techniques for DNA Sequence Data
... of biological sequence ...DNA sequence data for better understanding and compression and it can change the upturned catalog of this standard procedure to an extra flattened ...
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Comparative analysis of Data Compression and Pattern Matching Techniques for Biological Big Data
... using data from ordinary corpus that held data from multiple sources, large corpus having file size >1MB including ...E.Coli sequence, and two text files, and an artificial corpus having files ...
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Hypergeometric analysis of tiling-array and sequence data: detection and interpretation of peaks
... requires data dragging between tools to relate the ROIs to information present in databases, such as gene-ontology, pathway information, or enrichment of certain genomic ...hypergeometric analysis of ...
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Effective Use of Data Mining on Biological and Clinical Data Analysis
... In the new feature space, we conduct feature selection and train SVM on 312 true PASes and same number of false PASes. The 10-fold cross-validation results on training data are 81.7% sensitivity with 94.1% ...
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Flexible Information Visualization of Multivariate Data from Biological Sequence Similarity Searches
... the data and the visualiza- tion. Since the data is multidimensional and the graphical system is three-dimensional, we inevitably overload the dimensionality of the screen when we map the data to the ...
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Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience
... linkage analysis in these families and used whole genome sequence (WGS) data from resilient individuals to interrogate identified linkage regions for candidate ...
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NOVEL ALGORITHMS AND SOFTWARE FOR BIOLOGICAL SEQUENCE ANALYSIS
... Working with proteins does not require reverse complements to be calculated, although it does pose its own set of intricacies using the bit representation. Since there are only 4 nucleotides for DNA, they are easily ...
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Application of Statistical Mirroring in Biological Sequence Analysis
... the analysis of biological sequences due to an increasing interest in bioinformatics ...big data management ...Big data of biological sequences necessitate for more complex mathematical ...
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Accessing and distributing EMBL data using CORBA (common object request broker architecture)
... An industry standard, the Object Management Groups (OMG) common object request broker architecture (CORBA), provides platform-independent programming interfaces and models for portable distributed object-ori- ented ...
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Domain adaptation algorithms for biological sequence classification
... labeled data needed with supervised al- gorithms is to use domain ...unlabeled data with all the features from the target domain to build a classifier for the target ...labeled data from the target ...
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Evaluating methods for the analysis of rare variants in sequence data
... Paramount among the problems of the rare variant methods was an inflated false-positive rate. Our analyses suggest a number of gene-specific characteristics and sam- ple characteristics that contribute to the increased ...
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Real Time Analysis and Visualization of Pathogen Sequence Data
... phylodynamic/phylogeographic analysis of 1,000 se- quences of 10-kb length takes on the order of 1 hour on a standard laptop ...WGS data. Bacterial WGS data typically come in the form of millions of ...
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Uncertainty and Sensitivity Analysis of Dynamic Biological Systems under Data Sparseness.
... experimental data, 2) the optimization routine used to fit the data to the model and/or 3) the uncertainty in the initial conditions for the gene expression ...
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Using rule based machine learning for candidate disease gene prioritization and sample classification of cancer gene expression data
... Microarray data analysis has been shown to provide an effective tool for studying cancer and genetic ...microarray analysis such as small sample sizes, a large attribute space and high noise levels ...
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ArachnoServer: a database of protein toxins from spiders
... evant data from the ...Most data- base fields can be searched, including all basic search fields, as well as additional features such as biological activity, posttranslational modifications, ...
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ANALYZING THE USES OF DATA MINING IN BIOLOGICAL AND ENVIRONMENTAL PROBLEMS
... of data are serene daily. Analyzing such data is a very key ...need. Data mining can meet this need by providing tools; methods and techniques to discover knowledge from real data ...how ...
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