Key Features

  • Creating, editing, and annotating nucleic acid and protein sequences
  • Searching 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+ search
  • Restriction analysis with the integrated REBASE restriction enzyme database
  • Integrated Primer3 package for PCR primer design
  • Searching for direct, inverted, and tandem repeats in DNA sequences
  • Constructing dot plots for nucleic acid sequences
  • Searching 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
  • Searching for ORFs
  • Cloning in silico
  • 3D structure viewer for files in PDB and MMDB formats, with anaglyph view support
  • Protein secondary structure prediction with GOR IV and PSIPRED algorithms
  • HMMER2 and HMMER3 package integration
  • Building (using integrated PHYLIP and MrBayes packages) and viewing phylogenetic trees
  • Local sequence alignment with the optimized Smith-Waterman algorithm
  • Combining various algorithms into custom workflows with UGENE Workflow Designer
  • Searching 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 the UGENE Assembly Browser
  • PCR in silico
  • Spade de novo assembler
« About UGENE User Interface »