UGENE Features

• Creating, editing, and annotating nucleic acid and protein sequences
• Fast search in a sequence
• Multiple sequence alignment: ClustalW, ClustalO, MUSCLE, Kalign, MAFFT, T-Coffee
• PCR in silico
• Search through online databases: NCBI, PDB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, DAS servers
• Local and NCBI Genbank BLAST search
• Open reading frames finder
• Restriction enzyme finder with integrated REBASE restriction enzymes list
• Integrated Primer3 package for PCR primer design
• Plasmid construction and annotation
• Cloning in silico by designing cloning vectors
• Genome mapping short reads with Bowtie, BWA, and UGENE Genome Aligner
• Raw NGS data processing
• Visualization of next-generation sequencing data (BAM files) using UGENE Assembly Browser
• Variant calling with SAMtools
• RNA-seq data analysis with Tuxedo pipeline (TopHat, Cufflinks, etc.)
• SPAdes de novo assembler
• HMMER2 and HMMER3 packages integration
• Chromatogram viewer
• Search for transcription factor binding sites (TFBS) with weight matrix and SITECON algorithms
• Search for direct, inverted, and tandem repeats in DNA sequences
• Local sequence alignment with optimized Smith-Waterman algorithm
• Building (using integrated IQ-TREE, PHYLIP Neighbor Joining, MrBayes or PhyML Maximum Likelyhood) and editing phylogenetic trees
• Combining various algorithms into custom workflows with UGENE Workflow Designer
• Contigs assembly with CAP3
• 3D Structure viewer for files in PDB and MMDB formats, anaglyph view support
• Protein secondary structure prediction with GOR IV and PSIPRED algorithms
• Constructing dotplots for nucleic acid sequences
• mRNA alignment with Spidey
• Search for a pattern of various algorithms’ results in a nucleic acid sequence with UGENE Query Designer