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  • 1
    In: Bioinformatics, 2010, Vol. 26(8), pp.1122-1124
    Description: Summary: Ergatis is a flexible workflow management system for designing and executing complex bioinformatics pipelines. However, its complexity restricts its usage to only highly skilled bioinformaticians. We have developed a web-based prokaryotic genome annotation server, Integrative Services for Genomics Analysis (ISGA), which builds upon the Ergatis workflow system, integrates other dynamic analysis tools and provides intuitive web interfaces for biologists to customize and execute their own annotation pipelines. ISGA is designed to be installed at genomics core facilities and be used directly by biologists. ISGA is accessible at and the system is also freely available for local installation. 〈p〉〈bold〉Contact:〈/bold〉 〈email〉qunfeng.dong@unt.edu〈/email〉〈/p〉 are available at online.
    Keywords: Biology;
    ISSN: 1367-4803
    E-ISSN: 1460-2059
    E-ISSN: 13674811
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  • 2
    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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  • 3
    In: Bioinformatics, 2009, Vol. 25(12), pp.1550-1551
    Description: Summary: 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 and the system is also freely available for local installations. 〈p〉〈bold〉Contact:〈/bold〉 〈email〉dongq@indiana.edu〈/email〉〈/p〉
    ISSN: 1367-4803
    E-ISSN: 1460-2059
    Source: Oxford University Press
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  • 4
    In: International Immunology, 2006, Vol.18(1), pp.19-29
    Description: Murine IL-4 is a pleiotropic cytokine with undefined core functional region for eliciting downstream signaling. We used molecular modeling to predict the binding sites recognized by an anti-IL-4-neutralizing mAb (11B.11) and peptide phage display to delineate their makeup. The results of these approaches were confirmed by site-directed mutagenesis analysis. The results suggest that the amino acid residues spanning from 79 to 86 (QRLFRAFR) on IL-4 are of the major binding site for 11B.11. Furthermore, the functional experiments demonstrate that the residues R80, R83 and R86, which are located in the helix C of murine IL-4, play a crucial role in binding to the IL-4R -chain. Taken together, a new core functional region of murine IL-4 is identified, which provides new insight into the interaction between IL-4 and IL-4R. In addition, the results demonstrate that 11B.11 binds to a core functional region of murine IL-4, which prevents this cytokine from interacting with its cognate receptor.
    Keywords: Site-Directed Mutagenesis ; Interleukin 4 ; Monoclonal Antibodies ; Phage Display ; Peptides ; Signal Transduction ; Cytokines and Chemokines ; Mice;
    ISSN: 0953-8178
    E-ISSN: 1460-2377
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