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Unipro UGENE User Manual

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Created by Yuliya Algaer on Dec 03, 2020

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About Unipro
About UGENE
Key Features
User Interface
High Performance Computing
Cooperation
Download and Installation
System Requirements
Installation on Windows
Installation on macOS
Installation on Linux
Data Analysis Tools
Reference Data for NGS
Configure Data for Metagenomics Classification
Configure ChIP-Seq Analysis Data
Basic Functions
UGENE Terminology
UGENE Window Components
Start Page
Project View
Task View
Log View
Notifications
Main Menu Overview
Creating New Project
Creating Document
Renaming Object
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 Amino Acid Translation
Export Sequences Associated with Annotation
Using Bookmarks
Exporting Project
Search in Project
Options Panel
Plugins Viewer
Searching NCBI Genbank
Fetching Data from Remote Database
UGENE Application Settings
General
Resources
Network
File Format
Directories
Logging
Alignment Color Scheme
External Tools
Supported External Tools
Custom External Tools
Workflow Designer Settings
OpenCL
Sequence View
Sequence View Components
Global Actions
Sequence Toolbars
Sequence Overview
Zoom View
Details View
Information about Sequence
Manipulating Sequence
Show/Hide Sequence View Components
Showing Sequence in Multiple Lines
Translating Nucleotide Sequence
Zooming Sequence
Creating New Ruler
Going To Position
Selecting Sequence Region
Copying and Pasting Sequence
Editing Sequence
Searching in Sequence
Exporting Selected Sequence Region
Exporting Sequence of Selected Annotations
Exporting Sequence Image
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
Highlight Region on 3D Structure
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
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
Consensus
Export Consensus
Alignment Overview
Working with Alignment
Selecting Alignment Region
Moving Subalignment
Copying and Pasting Subalignment
Searching in Alignment
Editing Alignment
Converting Alignemnt
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
Removing All Gaps
Undo and Redo Framework
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
Importing APR and ACE Files
Realigning sequence(s) to other sequences
Statistics
Distance Matrix
Grid Profile
Advanced Functions
Building HMM Profile
Building Phylogenetic Tree
PHYLIP Neighbor-Joining
MrBayes
PhyML Maximum Likelihood
Phylogenetic Tree Viewer
Tree Settings
Selecting Tree Layout and View
Modifying Labels Appearance
Showing and Hiding Labels
Aligning Labels
Changing Labels Formatting
Adjusting Branch Settings
Zooming Tree
Working with Clade
Selecting Clade
Collapsing and Expanding Branches
Swapping Siblings
Zooming Clade
Adjusting Clade Settings
Changing Root
Exporting Tree Image
Printing Tree
Sanger Reads Editor
Sanger Reads Editor Overview
Sanger Reads Editor Features
Sanger Reads Editor Components
Working with Chromatogram
Mapping Reads to Reference
Alignment Statistics
Alignment Appearance
Overview and Show and Hide Chromatogram
Sanger Reads Consensus
Export Chromatogram Consensus
Navigation in Sanger Reads Alignment
Editing Sanger Reads
Inserting Character
Replacing Character and Gap
Removing Character and Gap
Inserting Gap
Removing Gap at the Left
Removing All Columns of Gaps
Trimming Left End
Trimming Right End
Renaming Read
Removing Read
Undo and Redo
Exporting Alignment without Chromatograms
Assembly Browser
Import BAM and SAM Files
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
Exporting Assembly Region
Options Panel in Assembly Browser
Navigation in Assembly Browser
Assembly Statistics
Assembly Browser Settings
Assembly Browser Hotkeys
Assembly Overview Hotkeys
Reads Area Hotkeys
Workflow Designer
About the Workflow Designer
Introduction
Launching Workflow Designer
Workflow Designer Window Components
Workflow Elements and Connections
Managing Parameters
UGENE Components and Workflow Designer
Task View, Notifications and Log View
Actions Menu
Toolbar
Context Menus
Application Settings
How to Create and Run Workflow
How to Use Sample Workflows
Manipulating Element
Adding Element
Copying Element
Pasting Element
Cutting Element
Deleting Element
Selecting All Elements on Scene
Manipulating Workflow
Creating New Workflow
Loading Workflow
Saving Workflow
Exporting Workflow as Image
Validating Workflow
Running Workflow
Dashboard
Dashboard Window Components
Using Dashboard
Stopping and Pausing Workflow
Changing Appearance
Custom Elements with Scripts
Functions Supported for Multiple Alignment Data
Functions Supported for Sequence Data
Functions Supported for Set of Annotations Data
Functions Supported for Files
Common Function
Custom Elements with External Tools
Creating Element
Editing Element
Adding Existent Element
Removing Element
Using Script to Set Parameter Value
Running Workflow from the Command Line
Running Workflow in Debugging Mode
Creating Breakpoints
Manipulating Breakpoints
Workflow File Format
Header
Body
Elements
Dataflow
Metainformation
Workflow Elements
Data Readers
Read Alignment Element
Read Annotations Element
Read FASTQ File with SE Reads Element
Read FASTQ Files with PE Reads Element
Read File URL(s) Element
Read NGS Reads Assembly Element
Read Plain Text Element
Read Sequence Element
Read Sequence from Remote Database Element
Read Variants Element
Data Writers
Write Alignment Element
Write Annotations Element
Write FASTA Element
Write NGS Reads Assembly Element
Write Plain Text Element
Write Sequence Element
Write Variants Element
Data Flow
Filter Element
Grouper Element
Multiplexer Element
Sequence Marker Element
Basic Analysis
Amino Acid Translation Element
Annotate with UQL Element
CD-Search Element
Collocation Search Element
Export PHRED Qualities Element
Fetch Sequences by ID From Annotation Element
Filter Annotation by Name Element
Filter Annotations by Qualifier
Find Correct Primer Pairs Element
Find Pattern Element
Find Repeats Element
Gene-by-gene approach report
Get Sequences by Annotations Element
Group Primer Pairs Element
Import PHRED Qualities Element
Intersect Annotations Element
Local BLAST+ Search Element
Merge Annotations Element
ORF Marker Element
Remote BLAST Element
Sequence Quality Trimmer Element
Smith-Waterman Search Element
Data Converters
Convert bedGraph Files to bigWig Element
Convert Text to Sequence Element
File Format Conversion Element
Reverse Complement Element
Split Assembly into Sequences Element
DNA Assembly
Assembly Sequences with CAP3
HMMER2 Tools
HMM2 Build Element
HMM2 Search Element
Read HMM2 Profile Element
Write HMM2 Profile Element
HMMER3 Tools
HMM3 Build Element
HMM3 Search Element
Read HMM3 Profile
Write HMM3 Profile
Multiple Sequence Alignment
Align Profile to Profile with MUSCLE Element
Align with ClustalO Element
Align with ClustalW Element
Align with Kalign Element
Align with MAFFT Element
Align with MUSCLE Element
Align with T-Coffee Element
Extract Consensus from Alignment as Sequence
Extract Consensus from Alignment as Text
In Silico PCR Element
Join Sequences into Alignment Element
Map to Reference Element
Split Alignment into Sequences Element
NGS: Basic Functions
CASAVA FASTQ Filter Element
Cut Adapter Element
Extract Consensus from Assembly Element
Extract Coverage from Assembly Element
FASTQ Merger Element
FASTQ Quality Trimmer Element
FastQC Quality Control Element
Filter BAM/SAM Files Element
Genome Coverage Element
Improve Reads with Trimmomatic Element
Merge BAM Files Element
Remove Duplicates in BAM Files Element
Slopbed Element
Sort BAM Files Element
NGS: ChIP-Seq Analysis
Annotate Peaks with peak2gene Element
Build Conservation Plot Element
Collect Motifs with SeqPos Element
Conduct GO Element
Create CEAS Report Element
Find Peaks with MACS Element
NGS: Map/Assemble Reads
Assemble Reads with SPAdes Element
Map Reads with Bowtie Element
Map Reads with Bowtie2 Element
Map Reads with BWA Element
Map Reads with BWA-MEM Element
Map Reads with UGENE Genome Aligner Element
Map RNA-Seq Reads with TopHat Element
NGS: Metagenomics Classification
Build CLARK Database
Build DIAMOND Database Element
Build Kraken Database Element
Classification Report Element
Classify Sequences with CLARK Element
Classify Sequences with DIAMOND Element
Classify Sequences with Kraken Element
Classify Sequences with MetaPhlAn2 Element
Ensemble Classification Data Element
Filter by Classification Element
Improve Classification with WEVOTE Element
NGS: RNA-Seq Analysis
Assemble Transcripts with StringTie Element
Assembly Transcripts with Cufflinks Element
Extract Transcript Sequences with gffread Element
Merge Assemblies with Cuffmerge Element
StringTie Gene Abudance Report Element
Test for Diff. Expression with Cuffdiff Element
NGS: Variant Analysis
Call Variants with SAMtools Element
Change Chromosome Notation for VCF Element
Convert SnpEff Variations to Annotations Element
Create VCF Consensus Element
SnpEff Annotation and Filtration Element
Transcription Factor
Build Frequency Matrix Element
Build SITECON Model Element
Build Weight Matrix Element
Convert Frequency Matrix Element
Read Frequency Matrix Element
Read SITECON Model Element
Read Weight Matrix Element
Search for TFBS with SITECON Element
Search for TFBS with Weight Matrix Element
Write Frequency Matrix Element
Write SITECON Model Element
Write Weight Matrix Element
Utils
DNA Statistics Element
Generate DNA Element
Workflow Samples
Alignment
Align Sequences with MUSCLE
Extract Consensus as Sequence
Extract Consensus as Text
Conversions
Convert "seq/qual" Pair to FASTQ
Convert Alignments to ClustalW
Convert UQL Schema Results to Alignment
Convert Sequence to Genbank
Custom Elements
CASAVA FASTQ Filter
FASTQ Trimmer
Dump Sequence Info
LinkData Fetch
Quality Filter
Data Marking
Marking by Annotation Number
Marking by Length
Data Merging
Find Substrings in Sequences
Merge Sequences and Shift Corresponding Annotations
Search for TFBS
HMMER
Build HMM from Alignment and test it
Search Sequences with Profile HMM
NGS
ChIP-Seq Coverage
ChIP-seq Analysis with Cistrome Tools
Extract Consensus from Assembly
Extract Coverage from Assembly
Extract Transcript Sequences
Quality Control by FastQC
De novo Assemble Illumina PE Reads
De novo Assemble Illumina PE and Nanopore Reads
De novo Assemble Illumina SE Reads
De Novo Assembly and Contigs Classification
Parallel NGS Reads Classification
Serial NGS Reads Classification
RNA-Seq Analysis with TopHat and StringTie
RNA-seq Analysis with Tuxedo Tools
Variation Annotation with SnpEff
Call Variants with SAMtools
Variant Calling and Effect Prediction
Raw ChIP-Seq Data Processing
Raw DNA-Seq Data Processing
Raw RNA-Seq Data Processing
Get Unmappet Reads
Sanger Sequencing
Trim and Align Sanger Reads
Scenarios
Filter Sequence That Match a Pattern
Search for Inverted Repeats
Find Patterns
Gene-by-gene Approach for Characterization of Genomes
Group Primer Pairs
Intersect Annotations
Filter out Short Sequences
Merge Sequences and Annotations
In Silico PCR Sample
Remote BLASTing
Get Amino Translations of a Sequence
Transcriptomics
Search for Transcription Factor Binding Sites (TFBS) in Genomic Sequences
Query Designer
About the Query Designer
Query Designer Introduction
Launching the Query Designer
Terminology
Query Designer Window Components
Schema Elements
How to Create and Run Schema
Manipulating Query Designer Element
Adding Algorithm Element
Adding Constraint Element
Renaming Algorithm Element
Resizing and Moving Algorithm Element
Managing of Elements Parameters
Changing Algorithm Element Appearance
Deleting Query Designer Element
Manipulating Schema
Creating New Schema
Loading Schema
Saving Schema
Changing Schema Appearance
Setting Order of Algorithms Execution
Managing Strands
Element Direction in Schema
Querying Sequence Strands
Running Schema from the Query Designer
Running Schema from the Sequence View
Query Designer Schema File Format
Header Query Designer Element
Body Query Designer Element
Element Description
Algorithm Element Description
Constraint Element Description
Metainformation Query Designer Element
Query Elements
Algorithm Elements
CDD Algorithm Element
Base Content Algorithm Element
Gc Content Algorithm Element
HMM3 Algorithm Element
ORF Algorithm Element
Primer Algorithm Element
Repeats Algorithm Element
Restriction Sites Algorithm Element
Pattern Algorithm Element
SITECON Algorithm Element
Smith-Waterman Algorithm Element
Tandem Repeats Algorithm Element
Weight Matrix Algorithm Element
HMM2 Algorithm Element
Constraint Elements
End-Start Constraint Element
Start-End Constraint Element
End-End Constraint Element
Start-Start Constraint Element
Extensions
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+
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 HMM2 Model
Calibrating HMM2 Model
Searching Sequence Using HMM2 Profile
HMM3
Building HMM Model
Searching Sequence Using HMM Profile
Searching Sequence Against Sequence Database
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 and cDNA
External Tools Plugin
Configuring External Tool
Plasmid Auto Annotation
ClustalO
Kalign Aligning
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
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

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