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Ugene Bioinformatics software


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Ugene Bioinformatics software

  1. 1. Outline Key Features Alignment Editor Phylogenetic Tree Viewer User Interface Sequence View Extensions Distributed Computing Fetching Data from Remote Database Sequence View Components Plugins
  2. 2. 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.
  3. 3. 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.
  4. 4. 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
  5. 5. Fetch Data from Remote Database
  6. 6. Sequence View Components
  7. 7. 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
  8. 8. Circular Viewer This Plug-in provides capability to show circular view of a nucleotide sequence.
  9. 9. 3D Structure Viewer This is opened automatically when you open a PDB or MMDB file.
  10. 10. Chromatogram Viewer This plug-in brings DNA chromatogram data viewing and editing capabilities into UGENE. Currently supported chromatogram file formats are ABIF and SCF.
  11. 11. Viewing Two Chromatograms Simultaneously
  12. 12. DNA Graph Package
  13. 13. DNA Graph Package
  14. 14. 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.
  15. 15. 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.
  16. 16. Alignment Editor Components
  17. 17. 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
  18. 18. Phylogenetic Tree Viewer
  19. 19. 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.
  20. 20. 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
  21. 21. 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.
  22. 22. References       Unipro UGENE version 1.12.2 ee_viewer.html or/overview/components.html w_extensions.html w_extensions/chromatogram_viewer/ ml Bioinformatics-2012-Okonechnikov-bioinformatics_bts091