Date post: | 03-Jul-2015 |
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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
Bioinformatics-2012-Okonechnikov-bioinformatics_bts091