UGENE is a free open-source bioinformatics software suite that allows users to analyze genomic and sequence data. It provides tools for tasks like sequence alignment and annotation, phylogenetic tree building, primer design, and in silico cloning. The software includes features like an alignment editor, sequence viewer, phylogenetic tree viewer, and tools integrated from packages like BLAST, HMMER, and PHYLIP. It also supports plugins that extend its functionality and allows distributed computing on cloud resources.

2. Outline
Key Features
Alignment
Editor
Phylogenetic
Tree Viewer
User Interface
Sequence
View
Extensions
Distributed
Computing
Fetching Data
from Remote
Database
Sequence
View
Components
Plugins

3. Key Features of UGENE
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A free cross-platform genome analysis suite.
Creating, Editing, Annotating.
Search through online Databases.
Multiple Sequence Alignment.
Online and local BLAST search.
Constructing dot plots for nucleic acid sequences.
Search for (TFBS) with weight matrix and SITECON
algorithms.
Aligning short reads with Bowtie and UGENE genome
aligner.

4. Key Features of UGENE
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Search for ORFs.
Cloning in silico.
3D structure viewer for files in PDB and MMDB formats.
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.

5. User Interface
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Visual and interactive genome browsing including
circular plasmid view
Multiple alignment editor
Chromatograms visualization
3D viewer for files in PDB and MMDB formats with
anaglyph stereo mode support
Phylogenetic tree viewer

6. Fetch Data from Remote
Database

7. Sequence View
Components

9. Sequence View
Extensions
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The functionality of the Sequence View can be
significantly increased with Sequence View Extensions.
The Circular Viewer shows the circular view of a
sequence
The 3D Structure Viewer adds 3D visualization for PDB
and MMDB files.
The Chromatogram Viewer adds support for
chromatograms visualization and editing
The DNA Graphs Package shows various graphs for
sequences
The Dot plot provides a tool to build dot plots for DNA
or RNA sequences

10. Circular Viewer
This Plug-in provides capability to show circular view of a nucleotide sequence.

11. 3D Structure Viewer
This is opened automatically when you open a PDB or MMDB file.

12. Chromatogram Viewer
This plug-in brings DNA chromatogram data viewing and editing capabilities into
UGENE. Currently supported chromatogram file formats are ABIF and SCF.

13. Viewing Two Chromatograms
Simultaneously

14. DNA Graph Package

15. DNA Graph Package

16. Dotplot
This plugin provides a tool to build dotplots for DNA or RNA sequences. This allows to
compare these sequences graphically. Using a dotplot graphic, you can easily identify such
differences between sequences as mutations, inversions, insertions, deletions and lowcomplexity regions.

18. Alignment Editor
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Perform multiple sequence alignment using
integrated MUSCLE and KAlign algorithms.
Edit an alignment: delete/copy/paste symbols,
sequences and sub-alignments.
Build phylogenetic trees.
Generate grid profiles.
Build Hidden Markov Model profiles to use with
HMM2/HMM3 tools.

19. Alignment Editor Components

20. Phylogenetic Tree Viewer
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Two methods for building phylogenetic trees are
supported:
 1. The PHYLIP Neighbour-Joining method.
 2. The MrBayes external tool.
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The following parameters are available:
Distance matrix model — model to compute a distance matrix.
The following values are available for a nucleotide multiple
sequence alignment:
• F84 (Distance Matrix)
• Kimura
• Jukes-Cantor
• LogDet

21. Phylogenetic Tree Viewer

22. Distributed Computing
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Distributed computing allows to notably increase
the performance of computational tasks by
distributing the task data among computational
units.
Cloud Computing
 Basically a cloud is a cluster of virtual servers
available over the Internet.
 One can use these servers to execute specific
functions: storage, computation etc.
 UGENE provides for users capability to launch
their computational tasks on the cloud.

23. Plug-ins
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An add-on piece of software that extends the
features or functionality of a larger application
 Workflow Designer
 DNA Annotator
 ORF Maker
 Restriction Analysis
 Molecular Cloning in silico
 Secondary Structure Prediction
 Smith-Waterman Search
 HMM2, HMM3, uMUSCLE, Bowtie, BWA,
UGENE Genome Aligner
 CAP3, Primer3

24. Conclusion
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Unipro UGENE is a vast suite for different
functions, methods and techniques. UGENE helps
a lot in understanding the sequences and their
alignment, It also provide ease to build trees and
view them. In silico molecular cloning is also an
important feature of UGENE.

25. References
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Unipro UGENE version 1.12.2
http://ugene.unipro.ru/documentation/manual/phylogenetic_tr
ee_viewer.html
http://ugene.unipro.ru/documentation/manual/alignment_edit
or/overview/components.html
http://ugene.unipro.ru/documentation/manual/sequence_vie
w_extensions.html
http://ugene.unipro.ru/documentation/manual/sequence_vie
w_extensions/chromatogram_viewer/view_simultaneously.ht
ml
Bioinformatics-2012-Okonechnikov-bioinformatics_bts091