Unipro UGENE
Science
Description:

UGENE is a free bioinformatics tool for DNA and protein sequence analysis


Version 1.10 features:

  • Visual annotation editor for DNA and protein sequences

  • Support for a number of popular bioinformatics data formats

  • Chromatograms visualization and editing

  • ORFs highlighting

  • NCBI databases integration (supports requests to BLAST and CDD services)

  • Multiple sequence alignment with graphical port of MUSCLE3, CLUSTAL, MAFFT, T-COFFEE and KAlign tools

  • Easy-to-use search with HMM profiles using graphical interface for HMMER2 and HMMER3 packages

  • 3D molecular protein and DNA structure viewer for PDB format

  • Assembly viewer. Fast with huge BAM and SAM files!

  • Built-in short reads aligners for all platforms: BOWTIE, BWA, UGENE aligner

  • Translation and back translation for DNA and protein alphabets

  • Workflow Designer to build complex reusable computational tasks

  • Query Designer to draw complex queries to genomes with mouse only

  • Search for Transcription Factor Binding Sites (TFBS) in DNA sequences

  • Huge files support, native support of gzipped documents

  • Restriction enzymes search and integration with REBASE restrictions enzymes database

  • Search for direct and inverted repeats in DNA sequences

  • A complete Smith-Waterman algorithm implementation

  • A visual interface for Phylip 3.6 and MrBayes package

  • Blast and Blast+ packages support

  • Ability to run tasks on remove machines with UGENE installed

  • A visual interface for Primer 3 package

  • Support for "cloning in silico"

  • Built-in support for JASPAR and UniPROBE databases

  • Powerful command-line interface. Ability to create new shell commands with graphical Workflow Designer tools

  • An option to run computations in Amazon EC2 environment

  • Built-in CUDA and OpenCL support

  • Opensource. Prebuilt packages are available for Windows, Linux and MacOS X platforms


  • rusconi

    6 years ago

    Hello,

    I'm wondering why you include the zlib 3rd party library in the source tree. Is this library modified, compared to the Gailly and Adler source other than some cosmetic differences I saw ? Would your software run with the original library linked as a shared object ?

    Thank you for your attention and happy new year !

    Filippo

    Report

    mfursov

    6 years ago

    Yes it can work with the original package.
    Moreover with Linux distributions the original package is used by default.

    zlib is included mostly for Windows users to make the whole bundle is complete: only QT libs are required to build UGENE.

    Report

    rusconi

    6 years ago

    Hello, thanks for your reply.

    I was wondering if Debian GNU/Linux packages would be feasible. I have searched for such packages and did not find any. Are you aware of any official package for Debian ? I may start doing that packaging if there are no such packages already somewhere.

    Sincerely,

    Filippo

    Report

    mfursov

    6 years ago

    There is an Ubuntu package of UGENE: https://launchpad.net/ubuntu/+source/ugene

    I think Debian installer should be almost the same.

    We have no 'debian' package now because the release cycle of Debian is longer then the overall project age and it's not possible for us having more or less up-to-date version in the stable branch.So we provided binary package that must work on any Linux distribution: http://ugene.unipro.ru/download.html
    However moving to Debian 'testing' would also be a good progress :)

    Report

    Mystique

    6 years ago

    Compile with Qt Creator

    In file included from ../../../ugene-1.9.0/src/ugenem/src/main.cpp:14:
    ../../../ugene-1.9.0/src/ugenem/src/SendReportDialog.h:22: fatal error: ../_tmp/ui/ui_SendReportDialog.h: Datei oder Verzeichnis nicht gefunden
    compilation terminated.

    Problem with this code line:

    #include "../_tmp/ui/ui_SendReportDialog.h"

    Report

    mfursov

    6 years ago

    Hi, half of the UGENE team uses QT Creator tool to develop UGENE and we cann't reproduce the issue. So this issue looks like a local misconfiguration

    Could you check that the project can be successfully compiled from the shell with 'qmake -r / make' commands first?

    Report

    Hellhang

    6 years ago

    Nice work man! -)

    Report

    luizpaulo

    7 years ago

    Great Work!

    Report

    Filename Version Description Filetype Packagetype License Downloads Date Filesize Install
    Score 66%
    66.00 Likes
    34 Dislikes
    Details
    version
    1.10.4
    updated Apr 12 2012
    added Oct 30 2008
    downloads
    page views 446