- 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
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