From MetaCentrum
Jump to navigation Jump to search


Ugene is a tool for munipulation and annotation sequnce data. Key features:

  • Creating, editing and annotating nucleic acid and protein sequences
  • Search through online databases: NCBI, ENSEMBL, PDB, SWISS-PROT, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, UniProt(DAS), Ensembl Human Genes (DAS)
  • Multiple sequence alignment: ClustalW, ClustalO, MUSCLE, Kalign, MAFFT, T-Coffee
  • Online and local BLAST and 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, Bowtie 2, BWA, BWA-SW and UGENE Genome Aligner
  • Contig assembly with CAP3
  • 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 and MrBayes packages) 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
  • Visualization of next generation sequencing data (BAM files) using UGENE Assembly Browser
  • PCR in silico
  • Spade de novo assembler




Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/

to your script before loading a module. Then, you can list all versions of ugene and load default version of ugene as

module avail ugene/ # list available modules
module load ugene   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail ugene

and choose explicit version you want to use.