A complex genome analysis suite
UGENE is a comprehensive genome analysis suite that features multiple sequence alignment and a complex HMM builder and search module.
UGENE is a handy tool that also offers a visual and interactive genome browsing experience.
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.
- Chromatograms visualization;
- 3D viewer for files in PDB and MMDB formats;
- Multiple sequence alignment editor;
- Easy to use workflow designer for custom computational workflows.
- 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.
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