Outline

Key Features

User Interface

Fetching Data from Remote

Database

Sequence View

Components

Sequence View

Extensions

Alignment Editor

PhylogeneticTree Viewer

Distributed Computing

Plugins

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

algorithms.

Aligning short reads with Bowtie and UGENE genome

aligner.

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

PSIPRED algorithms.

HMMER2 and HMMER3 packages integration.

Building (using integrated PHYLIP package) and viewing

phylogenetic trees.

Local sequence alignment with optimized Smith-Waterman

algorithm.

User Interface

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

Fetch Data from Remote

Database

Sequence View

Components

Sequence View

Extensions 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

Circular ViewerThis Plug-in provides capability to show circular view of a nucleotide sequence.

3D Structure ViewerThis is opened automatically when you open a PDB or MMDB file.

Chromatogram Viewer This plug-in brings DNA chromatogram data viewing and editing capabilities into

UGENE. Currently supported chromatogram file formats are ABIF and SCF.

Viewing Two Chromatograms

Simultaneously

DNA Graph Package

DNA Graph Package

DotplotThis 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 low-

complexity regions.

Alignment Editor

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.

Alignment Editor Components

Phylogenetic Tree Viewer

Two methods for building phylogenetic trees are supported:

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 sequence alignment:

• F84 (Distance Matrix)

• Kimura

• Jukes-Cantor

• LogDet

Phylogenetic Tree Viewer

Distributed Computing

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.

Plug-ins

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

Conclusion

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.

References

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

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