UGENE
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Application data |
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| Created by | Unipro |
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| Biological application domain(s) | Phylogenetics, Genomics, Sequence analysis, Protein structure analysis |
| Principal bioinformatics method(s) | Sequence parsing |
| Technology | ABI SOLiD, Sanger, Illumina, 454 |
| Created at | Unipro, Russia |
| Maintained? | Yes |
| Input format(s) | FASTA, GenBank, EMBL, FASTQ, AB1, Stockholm, clustalw, fasta.gz, phylip, MSF, GFF, newick, ACE, SAM |
| Output format(s) | FASTA, GenBank, Stockholm, clustalw, fasta.gz, newick, ACE, SAM |
| Programming language(s) | C++ |
| Licence | GPLv3 |
| Operating system(s) | Linux, Windows, Mac OS X |
| Contact: | ugene@unipro.ru |
Summary: UGENE is a free cross-platform genome analysis suite that combines popular bioinformatics tools within a single user friendly interface.
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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.
Links
References
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