From Bioinformatics.Org Wiki
UGENE is a free cross-platform bioinformatics software package.
It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces. Using UGENE Workflow Designer one can arrange the required tools and algorithms into a workflow schema.
In order to provide maximum possible performance UGENE utilizes multicore CPUs and GPUs to optimize some of its computational routines. Another way to speed up computations is to use Amazon EC2 cloud resources.
The software supports the following features:
- Creating, editing and annotating nucleic acid and protein sequences
- Search through online databases: NCBI, PDB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
- Multiple sequence alignment: Clustal, MUSCLE, Kalign, MAFFT, T-Coffee
- Online and local BLAST search
- Restriction analysis with integrated REBASE restriction enzyme database
- Integrated Primer3 package for PCR primers design
- Search for direct, inverted and tandem repeats in DNA sequences
- Constructing dotplots for nucleic acid sequences
- Search for transcription factor binding sites (TFBS) with weight matrix and SITECON algorithms
- Aligning short reads with Bowtie and UGENE genome aligner
- Search for ORFs
- Cloning in silico
- 3D structure viewer for files in PDB and MMDB formats, anaglyph view support
- Protein secondary structure prediction with GOR IV and PSIPRED algorithms
- HMMER2 and HMMER3 packages integration
- Building (using integrated PHYLIP package) and viewing phylogenetic trees
- Local sequence alignment with optimized Smith-Waterman algorithm
- Combining various algorithms into custom workflows with UGENE Workflow Designer
- Search for a pattern of various algorithms’ results in a nucleic acid sequence with UGENE Query Designer
1. The Sequence view is used to visualize, analyze and modify nucleic acid or protein sequences. Depending on the sequence type and the options selected the followings views can be presented inside the Sequence view window:
2. The Alignment editor is used to visualize, analyze and modify a nucleic acid or protein multiple sequence alignment.
3. The Phylogenetic tree viewer.
UGENE Workflow Designer
UGENE Workflow Designer allows creating and running complex computational workflow schemas.
The elements that a schema consists of correspond to the bulk of algorithms integrated into UGENE. Using the Workflow Designer one can also create custom workflow elements.
UGENE Query Designer
UGENE Query Designer allows a user to analyze a nucleotide sequence using different algorithms (Repeats finder, ORF finder, Weight matrix matching, etc.) at the same time imposing constraints on the positional relationship of the results obtained from the algorithms.
Supported biological data formats
- Sequences and annotations: FASTA (.fa), GenBank (.gb), EMBL (.emb), GFF(.gff)
- Multiple sequence alignments: Clustal (.aln), MSF (.msf), Stockholm (.sto), Nexus (.nex)
- 3D structures: PDB (.pdb), MMDB (.prt)
- Chromatograms: ABIF (.abi), SCF (.scf)
- Short reads: Sequence Alignment/Map(SAM) (.sam), ACE (.ace), FASTQ (.fastq)
- Phylogenetic trees: Newick (.nwk)
- Other formats: Bairoch (enzymes info), HMM (HMMER profiles), PWM and PFM (position matrices), etc.
The features to be included into the next release are mostly initiated by users.
- Sequence alignment software
- Bioinformatics, Computational biology
- Free open source bioinformatics projects
- Discovery Studio
- Gene Designer
- Vector NTI
- CLC Main Workbench
- 2008. Multitasking software system for DNA analysis Proceedings of the Sixth International Conference on Bioinformatics of Genome Regulation and Structure 1():78. ()
- 2009. UGENE: interactive computational schemes for genome analysis Proceedings of the Fifth Moscow International Congress on Biotechnology 3():14–15. ()
- 2009. UGENE: high performance genome analysis suite Proceedings of the Fifth Moscow International Congress on Biotechnology 2():405–406. ()
- UGENE homepage
- UGENE podcast
- UGENE documentation
- UGENE forum