Key Features of UGENE
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
Aligning short reads with Bowtie and UGENE genome
Key Features of UGENE
Search for ORFs.
Cloning in silico.
3D structure viewer for files in PDB and MMDB formats.
Protein secondary structure prediction with GOR IV and
HMMER2 and HMMER3 packages integration.
Building (using integrated PHYLIP package) and viewing
Local sequence alignment with optimized Smith-Waterman
Visual and interactive genome browsing including
circular plasmid view
Multiple alignment editor
3D viewer for files in PDB and MMDB formats with
anaglyph stereo mode support
Phylogenetic tree viewer
The functionality of the Sequence View can be
signiﬁcantly increased with Sequence View Extensions.
The Circular Viewer shows the circular view of a
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
The Dot plot provides a tool to build dot plots for DNA
or RNA sequences
This Plug-in provides capability to show circular view of a nucleotide sequence.
3D Structure Viewer
This is opened automatically when you open a PDB or MMDB ﬁle.
This plug-in brings DNA chromatogram data viewing and editing capabilities into
UGENE. Currently supported chromatogram ﬁle formats are ABIF and SCF.
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.
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
Phylogenetic Tree Viewer
Two methods for building phylogenetic trees are
1. The PHYLIP Neighbour-Joining method.
2. The MrBayes external tool.
The following parameters are available:
Distance matrix model — model to compute a distance matrix.
The following values are available for a nucleotide multiple
• F84 (Distance Matrix)
Distributed computing allows to notably increase
the performance of computational tasks by
distributing the task data among computational
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.
An add-on piece of software that extends the
features or functionality of a larger application
Molecular Cloning in silico
Secondary Structure Prediction
HMM2, HMM3, uMUSCLE, Bowtie, BWA,
UGENE Genome Aligner
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.