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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




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