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