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  • 2009  (14)
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  • 2009  (14)
  • 1
    Language: English
    In: Bioinformation, 2009, Vol.3(7), pp.296-8
    Description: Richness is defined as the number of distinct species or classes in a sample or population. Although richness estimation is an important practice, it requires mathematical and computational methods that are challenging to understand and implement. We have developed a web server, RICHness ESTimator (RICHEST), which implements three non-parametric statistical methods for richness estimation. Its user-friendly web interface allows users to analyze and compare their data conveniently over the web. A web server hosting RICHEST is accessible at http://richest.cgb.indiana.edu/cgi-bin/index.cgi and the software is freely available for local installations.
    Keywords: Biological Data ; Complex ; Diversity Estimation ; Population ; Simple
    E-ISSN: 0973-2063
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  • 2
    In: Bioinformation, 2009, Vol.3(7), p.296-298
    Description: Richness is defined as the number of distinct species or classes in a sample or population. Although richness estimation is an important practice, it requires mathematical and computational methods that are challenging to understand and implement. We have developed a web server, RICHness ESTimator...
    Keywords: Web Server ; Diversity Estimation ; Biological Data ; Complex ; Simple ; Population
    E-ISSN: 0973-2063
    Source: U.S. National Library of Medicine (NIH/NLM)
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  • 3
    Language: English
    In: Bioinformatics (Oxford, England), 15 June 2009, Vol.25(12), pp.1550-1
    Description: The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users to upload genome annotation in the GFF3 format, configure the display of each genomic feature by simply using a web browser and visualize the configured genomic features with the integrated GBrowse software. WebGBrowse is accessible via http://webgbrowse.cgb.indiana.edu/ and the system is also freely available for local installations.
    Keywords: Software ; Computational Biology -- Methods ; Genome -- Genetics
    ISSN: 13674803
    E-ISSN: 1367-4811
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  • 4
    Language: English
    In: BMC Genomics, April 21, 2009, Vol.10, p.174
    Description: Background EST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no longer a bottleneck for investigators. However, processing large amounts of EST data remains a non-trivial challenge for many. Web-based EST analysis tools are proving to be the most convenient option for biologists when performing their analysis, so these tools must continuously improve on their utility to keep in step with the growing needs of research communities. We have developed a web-based EST analysis pipeline called ESTPiper, which streamlines typical large-scale EST analysis components. Results The intuitive web interface guides users through each step of base calling, data cleaning, assembly, genome alignment, annotation, analysis of gene ontology (GO), and microarray oligonucleotide probe design. Each step is modularized. Therefore, a user can execute them separately or together in batch mode. In addition, the user has control over the parameters used by the underlying programs. Extensive documentation of ESTPiper's functionality is embedded throughout the web site to facilitate understanding of the required input and interpretation of the computational results. The user can also download intermediate results and port files to separate programs for further analysis. In addition, our server provides a time-stamped description of the run history for reproducibility. The pipeline can also be installed locally, allowing researchers to modify ESTPiper to suit their own needs. Conclusion ESTPiper streamlines the typical process of EST analysis. The pipeline was initially designed in part to support the Daphnia pulex cDNA sequencing project. A web server hosting ESTPiper is provided at http://estpiper.cgb.indiana.edu/ to now support projects of all size. The software is also freely available from the authors for local installations.
    Keywords: Antisense Dna -- Physiological Aspects ; Antisense Dna -- Research ; Applications Software -- Usage ; Dna Sequencing -- Methods
    ISSN: 1471-2164
    Source: Cengage Learning, Inc.
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  • 5
    Language: English
    In: BMC Genomics, April 21, 2009, Vol.10, p.174
    Description: Background EST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no longer a bottleneck for investigators. However, processing large amounts of EST data remains a non-trivial challenge for many. Web-based EST analysis tools are proving to be the most convenient option for biologists when performing their analysis, so these tools must continuously improve on their utility to keep in step with the growing needs of research communities. We have developed a web-based EST analysis pipeline called ESTPiper, which streamlines typical large-scale EST analysis components. Results The intuitive web interface guides users through each step of base calling, data cleaning, assembly, genome alignment, annotation, analysis of gene ontology (GO), and microarray oligonucleotide probe design. Each step is modularized. Therefore, a user can execute them separately or together in batch mode. In addition, the user has control over the parameters used by the underlying programs. Extensive documentation of ESTPiper's functionality is embedded throughout the web site to facilitate understanding of the required input and interpretation of the computational results. The user can also download intermediate results and port files to separate programs for further analysis. In addition, our server provides a time-stamped description of the run history for reproducibility. The pipeline can also be installed locally, allowing researchers to modify ESTPiper to suit their own needs. Conclusion ESTPiper streamlines the typical process of EST analysis. The pipeline was initially designed in part to support the Daphnia pulex cDNA sequencing project. A web server hosting ESTPiper is provided at http://estpiper.cgb.indiana.edu/ to now support projects of all size. The software is also freely available from the authors for local installations.
    Keywords: Antisense Dna -- Physiological Aspects ; Antisense Dna -- Research ; Applications Software -- Usage ; Dna Sequencing -- Methods
    ISSN: 1471-2164
    Source: Cengage Learning, Inc.
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  • 6
    Language: English
    In: Bioinformation, pp. 296-298
    Description: Article discussing a web server for richness estimation in biological data called RICHness ESTimator (RICHEST).
    Keywords: Diversity Estimations ; Biological Data ; Complex ; Simple ; Populations
    Source: University of North Texas
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  • 7
    In: Bioinformatics, 2009, Vol. 25(7), pp.956-957
    Description: Summary: Investigating the conservation of gene clusters across multiple genomes has become a standard practice in the era of comparative genomics. However, all existing software and databases rely heavily on pre-computation to identify homologous genes by genome-wide comparisons. Such pre-computing strategies lack accuracy and updating the data is computationally intensive. Since most molecular biologists are often interested only in a small cluster of genes, catering to this need, we have developed a web-based software system that allows users to upload a list of genes, perform dynamic search against the genomes of their choices and interactively visualize the gene cluster conservation using a novel multi-genome browser. Our approach avoids expensive genome-wide pre-computing and allows users to dynamically change the search criteria to fit their genes of interest. Our system can be customized for any genome sequences. We have applied it to both prokaryotic and eukaryotic genomes to illustrate its usability. Our software is freely available at . 〈p〉〈bold〉Contact:〈/bold〉 〈email〉dongq@indiana.edu〈/email〉〈/p〉
    Keywords: Biology;
    ISSN: 1367-4803
    E-ISSN: 1460-2059
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  • 8
    Language: English
    In: BMC Genomics, 01 April 2009, Vol.10(1), p.174
    Description: Abstract Background EST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no longer a bottleneck for investigators. However, processing large amounts of EST data remains a non-trivial challenge for many. Web-based EST analysis tools are proving to be the most convenient option for biologists when performing their analysis, so these tools must continuously improve on their utility to keep in step with the growing needs of research communities. We have developed a web-based EST analysis pipeline called ESTPiper, which streamlines typical large-scale EST analysis components. Results The intuitive web interface guides users through each step of base calling, data cleaning, assembly, genome alignment, annotation, analysis of gene ontology (GO), and microarray oligonucleotide probe design. Each step is modularized. Therefore, a user can execute them separately or together in batch mode. In addition, the user has control over the parameters used by the underlying programs. Extensive documentation of ESTPiper's functionality is embedded throughout the web site to facilitate understanding of the required input and interpretation of the computational results. The user can also download intermediate results and port files to separate programs for further analysis. In addition, our server provides a time-stamped description of the run history for reproducibility. The pipeline can also be installed locally, allowing researchers to modify ESTPiper to suit their own needs. Conclusion ESTPiper streamlines the typical process of EST analysis. The pipeline was initially designed in part to support the Daphnia pulex cDNA sequencing project. A web server hosting ESTPiper is provided at http://estpiper.cgb.indiana.edu/ to now support projects of all size. The software is also freely available from the authors for local installations.
    Keywords: Biology
    ISSN: 1471-2164
    E-ISSN: 1471-2164
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  • 9
    Language: English
    In: IEEE INFOCOM 2009, April 2009, pp.2646-2650
    Description: Multi-hop wireless networks using directional antennas are increasingly deployed for various applications such as wireless backhaul. In such systems, each node is equipped with a few directional antennas. Each antenna is exclusively used for establishing a point-to-point link with another antenna on some neighboring node. Thus in the constructed network, each node cannot have more links than its number of installed antennas, which defines a degree bound on all nodes. Hence, a practically important problem is to construct fault resilient and high capacity networks with bounded node degree. The main contribution of this paper is two-fold. First, we propose a localized algorithm for building fault resilient wireless networks that contain the path with highest possible capacity for every pair of nodes, not only in normal cases but also in the presence of any node/link failure. Second, we give an algorithm for building fault resilient wireless networks with the lowest possible degree bound.
    Keywords: Wireless Networks ; Directional Antennas ; Peer to Peer Computing ; Spread Spectrum Communication ; Buildings ; Wireless Mesh Networks ; Network Topology ; Communications Society ; Computer Science ; Costs ; Engineering ; Computer Science
    ISBN: 9781424435128
    ISBN: 1424435129
    ISSN: 0743166X
    Source: IEEE Conference Publications
    Source: IEEE Xplore
    Source: IEEE Journals & Magazines 
    Source: IEEE eBooks
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  • 10
    Language: English
    In: BMC Genomics, London: BioMed Central Ltd.
    Description: Article discussing ESTPiper, a web interface that streamlines the expressed sequence tags (EST) analysis process.
    Keywords: Analysis Pipelines ; Expressed Sequence Tags ; Estpiper ; Genome Sequencing Technologies
    Source: University of North Texas
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