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Short description:
Please summarise the application in a few sentences. Avoid links here. UGENE is a free cross-platform genome analysis suite that combines popular bioinformatics tools within a single user friendly interface.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Phylogenetics, Genomics, Sequence analysis, Protein structure analysis
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Sequence parsing,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
ABI SOLiD, Sanger, Illumina, 454
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
Unipro, Russia
Main features: * Multiple sequence alignment using MUSCLE 3, MUSCLE 4 and KAlign; * 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; * Phylogenetic analysis with Phylip; * 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 (SSE2, CUDA); * Ability to run computational tasks on remote PCs User Interface: * Visual and interactive genome browsing; * Chromatograms visualization; * 3D viewer for files in PDB and MMDB formats with anaglyph stereo mode support; * 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. The tool uses Qt 4 as its GUI library.
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