- Creating, editing and
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- annotating nucleic
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- acid and protein
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- sequences
- Search
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- through online databases: NCBI,
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- ENSEMBL, PDB, SWISS-PROT, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, UniProt(DAS), Ensembl Human Genes (DAS)
- Multiple sequence alignment:
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- ClustalW, ClustalO, MUSCLE, Kalign, MAFFT, T-Coffee
- Online and
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- local BLAST and BLAST+ search
- Restriction analysis with integrated REBASE restriction enzyme database
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- Integrated Primer3
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- package for PCR
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- primers design
- Search
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- for direct, inverted and tandem repeats in DNA sequences
- Constructing dotplots for nucleic acid sequences
- Search
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- for transcription factor binding sites (TFBS)
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- with weight matrix
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- and SITECON
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- algorithms
- Aligning short reads
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- 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
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- algorithms' results in
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- a nucleic acid
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- sequence with UGENE Query Designer
- Visualization of next generation sequencing data (BAM files) using UGENE Assembly Browser