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  • Home / Linux / Science

    UGENE 1.5.2

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    UniPro | More programs
    GPL / FREE
    November 7th, 2009, 17:19 GMT [view history]
    ROOT / Science

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    UGENE description

     

    Integrated Bioinformatics Tools

    UGENE is a free cross-platform genome analysis suite.

    It works perfectly on Linux, Windows or Mac OS and requires only a few clicks to install.

    Here are some key features of "UGENE":

    Main features:

    · Multiple sequence alignment using MUSCLE 3 and MUSCLE 4;
    · HMM profiles build and search, based on the source of HMMER 2 and HMMER 3;
    · PCR Primers design using Primer 3;
    · Protein secondary structure prediction using GOR IV and PSIPRED;
    · Search for restriction enzymes and integration with REBASE;
    · Extremely fast repeat finder;
    · Search for transcription factor binding sites using SITECON;
    · ORF finder;
    · Complete Smith-Waterman algorithm implementation.

    User Interface:

    · Visual and interactive genome browsing;
    · Chromatograms visualization;
    · 3D viewer for files in PDB and MMDB formats;
    · Multiple sequence alignment editor;
    · Easy to use workflow designer for custom computational workflows.

    · High performance computing in UGENE

    · Complete support of modern multicore processors and SSE instructions;
    · Out of the box support of modern GPUs using NVIDIA CUDA and ATI Stream;
    · Integrated solutions for Cell Broadband Engine;
    · Private solutions for supercomputers and distributed computing.

    Cooperation:

    · Can be used for education in schools and universities;
    · Features to be included into the next release are initiated by users;
    · UGENE team is ready for collaboration in related projects, both free or commercial.

    Requirements:

    · Qt

    What's New in This Release: [ read full changelog ]

    New plugins:

    · MUSCLE 4 - a port of the newest tool for multiple sequence alignment by Robert C. Edgar;
    · CUDA Support - an utility plugin which makes possible using NVIDIA graphical processing units for accelerating computational algorithms.

    New features and bug fixes:

    · CUDA-accelerated Smith-Waterman algorithm is ready to use for Windows users;
    · The one of the most awaited features: sequence editing has been added;
    · Exporting annotation tables to CSV has been provided;
    · HMM2 models support has been added to HMM3;
    · And many others. See the changelog for a full list of improvements.

      


    TAGS:

    bioinformatics tools | genome analyzer | multiple sequence alignment | bioinformatics | genome | analyzer



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