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Unipro UGENE Online User Manual

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Created by Yuliya Algaer, last modified on Jan 09, 2014

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About Unipro
About UGENE
Key Features
User Interface
High Performance Computing
Cooperation
Download and Installation
System Requirements
UGENE Packages
Installation on Windows
Installation on Mac OS X
Installation on Linux
Native Installation on Ubuntu
Native Installation on Fedora
Basic Functions
UGENE Terminology
UGENE Window Components
Welcome Page
Project View
Task View
Log View
Notifications
Main Menu Overview
Creating New Project
Creating Document
Opening Document
Opening for the First Time
Advanced Dialog Options
Opening Document Present in Project
Opening Several Documents
Opening Unloaded Documents
Opening from Clipboard
Opening Containing Folder
Exporting Documents
Locked Documents
Using Objects and Object Views
Exporting Objects
Exporting Sequences to Sequence Format
Exporting Sequences as Alignment
Exporting Alignment to Sequence Format
Exporting Nucleic Alignment to Amino Translation
Export Sequences Associated with Annotation
Using Bookmarks
Exporting Project
Search in Project
Options Panel
Adding and Removing Plugins
Searching NCBI Genbank
Fetching Data from Remote Database
UGENE Application Settings
General
Resources
Network
File Format
Directories
Logging
Alignment Color Scheme
External Tools Settings
Genome Aligner
Workflow Designer Settings
OpenCL
Sequence View
Sequence View Components
Global Actions
Sequence Toolbars
Sequence Overview
Sequence Zoom View
Sequence Details View
Sequence Multi-line Details View
Information about Sequence
Manipulating Sequence
Going To Position
Toggling Views
Exporting Sequence Image
Zooming Sequence
Creating New Ruler
Selecting Amino Translation
Showing and Hiding Translations
Selecting Sequence
Copying/Pasting Sequence
Search in Sequence
Load Patterns from File
Search Algorithm
Search in
Other Settings
Annotations Settings
Editing Sequence
Exporting Selected Sequence Region
Exporting Sequence of Selected Annotations
Locking and Synchronize Ranges of Several Sequences
Multiple Sequence Opening
Annotations Editor
"db_xref" Qualifier
Automatic Annotations Highlighting
The "comment" Annotation
Manipulating Annotations
Creating Annotation
Selecting Annotations
Editing Annotation
Highlighting Annotations
Annotations Color
Annotations Visability
Show on Translation
Captions on Annotations
Creating and Editing Qualifier
Adding Column for Qualifier
Copying Qualifier Text
Finding Qualifier
Deleting Annotations and Qualifiers
Importing Annotations from CSV
Exporting Annotations
Sequence View Extensions
Circular Viewer
Circular View Settings
3D Structure Viewer
Opening 3D Structure Viewer
Changing 3D Structure Appearance
Selecting Render Style
Selecting Coloring Scheme
Calculating Molecular Surface
Selecting Background Color
Selecting Detail Level
Enabling Anaglyph View
Moving, Zooming and Spinning 3D Structure
Selecting Sequence Region
Selecting Models to Display
Structural Alignment
Exporting 3D Structure Image
Working with Several 3D Structures Views
Chromatogram Viewer
Exporting Chromatogram Data
Viewing Two Chromatograms Simultaneously
DNA/RNA Graphs Package
Description of Graphs
Graph Settings
Saving Graph Cuttoffs as Annotations
Dotplot
Creating Dotplot
Navigating in Dotplot
Zooming to Selected Region
Selecting Repeat
Interpreting Dotplot: Identifying Matches, Mutations, Invertions, etc.
Editing Parameters
Filtering Results
Saving Dotplot as Image
Saving and Loading Dotplot
Building Dotplot for Currently Opened Sequence
Comparing Several Dotplots
Alignment Editor
Overview
Alignment Editor Features
Alignment Editor Components
Navigation
Coloring Schemes
Creating Custom Color Scheme
Highlighting Alignment
Zooming and Fonts
Searching for Pattern
Consensus
Export Consensus
Alignment Overview
Working with Alignment
Undo/Redo Framework
Selecting Subalignment
Moving Subalignment
Copying/Pasting Subalignment
Editing Alignment
Removing Selection
Filling Selection with Gaps
Replacing Selected Character
Replacing with Reverse-Complement
Replacing with Reverse
Replacing with Complement
Removing Columns of Gaps
Removing Sequence(s)
Removing All Gaps
Saving Alignment
Aligning Sequences
Aligning Sequence to this Alignment
Pairwise Alignment
Working with Sequences List
Adding New Sequences
Renaming Sequences
Sorting Sequences
Shifting Sequences
Collapsing Rows
Copying Sequences
Exporting in Alignment
Extracting Selected as MSA
Exporting Sequence from Alignment
Exporting Alignment as Image
Statistics
Distance Matrix
Grid Profile
Advanced Functions
Building HMM Profile
Building Phylogenetic Tree
PHYLIP Neighbor-Joining
MrBayes
PhyML Maximum Likelihood
Assembly Browser
Import BAM/SAM File
Import ACE File
Browsing and Zooming Assembly
Opening Assembler Browser Window
Assembly Browser Window
Assembly Browser Window Components
Reads Area Description
Assembly Overview Description
Ruler and Coverage Graph Description
Go to Position in Assembly
Using Bookmarks for Navigation in Assembly Data
Getting Information About Read
Short Reads Vizualization
Reads Highlighting
Reads Shadowing
Associating Reference Sequence
Associating Variations
Consensus Sequence
Exporting
Exporting Reads
Exporting Visible Reads
Exporting Coverage
Exporting Consensus
Exporting Consensus Variations
Exporting Assembly as Image
Options Panel in Assembly Browser
Navigation in Assembly Browser
Assembly Statistics
Assembly Browser Settings
Assembly Browser Hotkeys
Assembly Overview Hotkeys
Reads Area Hotkeys
Phylogenetic Tree Viewer
Tree Settings
Selecting Tree Layout and View
Modifying Labels Appearance
Showing/Hiding Labels
Aligning Labels
Changing Labels Formatting
Adjusting Branch Settings
Zooming Tree
Working with Clade
Selecting Clade
Collapsing/Expanding Branches
Swapping Siblings
Zooming Clade
Adjusting Clade Settings
Changing Root
Exporting Tree Image
Printing Tree
Extensions
Workflow Designer
DNA Annotator
DNA Flexibility
Configuring Dialog Settings
Result Annotations
DNA Statistics
DNA Generator
ORF Marker
Remote BLAST
Exporting BLAST Results to Alignment
Fetching Sequences from Remote Database
BLAST/BLAST+
Creating Database
Making Request to Database
Fetching Sequences from Local BLAST Database
Repeat Finder
Repeats Finding
Tandem Repeats Finding
Tandem Repeats Search Result
Restriction Analysis
Selecting Restriction Enzymes
Using Custom File with Enzymes
Filtering by Number of Hits
Excluding Region
Circular Molecule
Results
Molecular Cloning in silico
Digesting into Fragments
Creating Fragment
Constructing Molecule
Available Fragments
Fragments of the New Molecule
Changing Fragments Order in the New Molecule
Removing Fragment from the New Molecule
Editing Fragment Overhangs
Reverse Complement a Fragment
Other Constuction Options
Output
Creating PCR Product
In Silico PCR
Primers Details
Primer Library
Secondary Structure Prediction
SITECON
SITECON Searching Transcription Factors Binding Sites
Types of SITECON Models
Eukaryotic
Prokaryotic
Building SITECON Model
Smith-Waterman Search
HMM2
Building HMM Model (HMM Build)
Calibrating HMM Model (HMM Calibrate)
Searching Sequence Using HMM Profile (HMM Search)
HMM3
Building HMM Model (HMM3 Build)
Searching Sequence Using HMM Profile (HMM3 Search)
Searching Sequence Against Sequence Database (Phmmer Search)
uMUSCLE
MUSCLE Aligning
Aligning Profile to Profile with MUSCLE
Aligning Sequences to Profile with MUSCLE
ClustalW
MAFFT
T-Coffee
Bowtie
Bowtie Aligning Short Reads
Building Index for Bowtie
Bowtie 2
Bowtie 2 Aligning Short Reads
Building Index for Bowtie 2
BWA
Aligning Short Reads with BWA
Building Index for BWA
BWA-SW
Aligning Short Reads with BWA-SW
Building Index for BWA-SW
BWA-MEM
Aligning Short Reads with BWA-MEM
Building Index for BWA-MEM
UGENE Genome Aligner
Aligning Short Reads with UGENE Genome Aligner
Building Index for UGENE Genome Aligner
Converting UGENE Assembly Database to SAM Format
CAP3
SPAdes
Weight Matrix
Searching JASPAR Database
Building New Matrix
Primer3
RTPCR Primer Design
Spliced Alignment (mRNA to genomic)
External Tools
Configuring External Tool
Query Designer
Plasmid Auto Annotation
ClustalO
Kalign Aligning
Expert Discovery
Loading Sequences
Mapping Sequences
Markup Sequences
Creating Signals
Generating Signals
Complex Signals Recognition on a Sequence
Shared Database
Configuring Database
Connecting to a Shared Database
Adding Data to the Database
Database in the Project
Deleting Data
Drag'n'drop in the Database
Exporting Objects from the Database
UGENE Public Storage
UGENE Command Line Interface
CLI Options
CLI Predefined Tasks
Format Converting Sequences
Converting MSA
Extracting Sequence
Finding ORFs
Finding Repeats
Finding Pattern Using Smith-Waterman Algorithm
Adding Phred Quality Scores to Sequence
Local BLAST Search
Local BLAST+ Search
Remote NCBI BLAST and CDD Requests
Annotating Sequence with UQL Schema
Building Profile HMM Using HMMER2
Searching HMM Signals Using HMMER2
Aligning with MUSCLE
Aligning with ClustalW
Aligning with ClustalO
Aligning with Kalign
Aligning with MAFFT
Aligning with T-Coffee
Building PFM
Searching for TFBS with PFM
Building PWM
Searching for TFBS with Weight Matrices
Building Statistical Profile for SITECON
Searching for TFBS with SITECON
Fetching Sequence from Remote Database
Gene-by-Gene Report
Reverse-Complement Converting Sequences
Variants Calling
Generating DNA Sequence
Creating Custom CLI Tasks
APPENDIXES
Appendix A. Supported File Formats
Specific File Formats
UGENE Native File Formats
Other File Formats
Tutorials
Using BioMart with UGENE
Environment requirements
Installing UGENE extension on Mozilla Firefox
Opening data found using BioMart in UGENE
Opening BioMart data in UGENE by ID
Opening selected data in UGENE

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