“…The w3DNA (web 3DNA) server is a user-friendly web-based interface to the 3DNA suite of programs for the analysis, reconstruction, and visualization of three-dimensional (3D) nucleic-acid-containing structures, including their complexes with proteins and other ligands. …”
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“…In essence, UniPrime2 is a suite of publicly available software packages (Blastn, T-Coffee, GramAlign, Primer3), which reduces the laborious process of primer design, by integrating these programs into a single software pipeline. …”
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“…Furthermore, we tested the prediction that the social organisation and limited powers of flight of Huia resulted in high levels of population genetic structure. Using a suite of microsatellite DNA loci, we report high levels of genetic diversity in Huia, and we detected no significant population genetic structure. …”
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“…To facilitate prion research, the PDDB also provides a suite of analytical tools for reconstructing dynamic networks via integration of temporal mRNA and interaction data and for analyzing these networks to generate hypotheses. …”
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“…In this report, we evaluate the efficiency of the generalized multifactor dimensionality reduction statistical suite to decipher small interacting factors that contribute to RA disease pathogenesis.…”
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“…Microarray profiling of wild type worms exposed to non-lethal hypertonicity identified a suite of genes that were also regulated by infection. …”
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“…A Python-based script suite, called PhyRe, has been developed to implement all analyses we describe in this paper. …”
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“…We have recently developed a novel method for the affinity purification of the complete suite of translating mRNA from genetically labeled cell populations. …”
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“…Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. …”
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“…The complete software suite is available for free download. Here we describe the software’s framework and provide details to guide users with development of this and similar software.…”
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“…It is made available as an independent software suite that can be downloaded and installed for local use. …”
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“…BACKGROUND: Fast ForWord is a suite of computer-based language intervention programs designed to improve children's reading and oral language skills. …”
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“…REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.…”
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“…We confirmed that degradation of the UFD but not the CRL2(VHL) or ubiquitin-independent substrates depends on p97 activity. We optimized our suite of assays to establish conditions suitable for high-throughput screening and then validated their performance by screening against 160 cell-permeable protein kinase inhibitors. …”
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“…In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. …”
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“…CONCLUSIONS AND SIGNIFICANCE: This protocol was implemented within the Rosetta3 software suite. To demonstrate and evaluate this protocol, we have developed a benchmarking set of structures from the PDB with loop-mediated interfaces. …”
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“…The R package ‘linkcomm’ implements this algorithm and extends it in several aspects: (i) the clustering algorithm handles networks that are weighted, directed, or both weighted and directed; (ii) several visualization methods are implemented that facilitate the representation of the link communities and their relationships; (iii) a suite of functions are included for the downstream analysis of the link communities including novel community-based measures of node centrality; (iv) the main algorithm is written in C++ and designed to handle networks of any size; and (v) several clustering methods are available for networks that can be handled in memory, and the number of communities can be adjusted by the user. …”
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“…Availability and implementation: The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. …”
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“…Scientists from diverse disciplines and locations around the world were joined through an integrated suite of collaborative technologies to exchange information on the latest developments in this area of origin of life research. …”
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“…Rosetta is one simulation suite that would benefit from a robust real-time visualization solution. …”
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