UGENE User Manual
- About Unipro
- About UGENE
- Download and Installation
- Basic Functions
- UGENE Terminology
- UGENE Window Components
- Main Menu Overview
- Creating New Project
- Creating Document
- Renaming Object
- Opening Document
- Opening Containing Folder
- Exporting Documents
- Locked Documents
- Using Objects and Object Views
- Exporting Objects
- Using Bookmarks
- Exporting Project
- Search in Project
- Saving Project
- Options Panel
- Plugins Viewer
- Searching NCBI Genbank
- Fetching Data from Remote Database
- UGENE Application Settings
- Sequence View
- Sequence View Components
- Global Actions
- Sequence Toolbars
- Sequence Overview
- Zoom View
- Details View
- Information about Sequence
- Manipulating Sequence
- Show and Hide Sequence View Components
- Showing Sequence in Multiple Lines
- Translating Nucleotide Sequence
- Zooming Sequence
- Creating a 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 Synchronizing Ranges of Several Sequences
- Multiple Sequence Opening
- Annotations Editor
- Manipulating Annotations
- Sequence View Extensions
- Circular Viewer
- 3D Structure Viewer
- Chromatogram Viewer
- Graphs Package
- Dotplot
- Creating Dotplot
- Navigating in Dotplot
- Zooming to Selected Region
- Selecting Repeat
- Interpreting Dotplot - Identifying Matches, Mutations, Inversions, 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
- Working with Alignment
- Selecting Alignment Region
- Moving Subalignment
- Copying and Pasting Subalignment
- Searching in Alignment
- Showing Alignment in Multiple Lines
- Editing Alignment
- Saving Alignment
- Aligning Sequences
- Adding Sequence(s) to Alignment
- Pairwise Alignment
- Working with Sequences List
- Exporting in Alignment
- Importing APR and ACE Files
- Realigning sequence(s) to other sequences
- Statistics
- Advanced Functions
- Building Phylogenetic Tree
- Phylogenetic Tree Viewer
- Sanger Reads Editor
- Assembly Browser
- Workflow Designer
- About the Workflow Designer
- Introduction
- Manipulating Element
- Manipulating Workflow
- Changing Appearance
- Custom Elements with Scripts
- Custom Elements with External Tools
- Using Script to Set Parameter Value
- Running Workflow from the Command Line
- Running Workflow in Debugging Mode
- Workflow File Format
- Workflow Elements
- Data Readers
- Data Writers
- Data Flow
- 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 Repeated Elements
- 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
- DNA Assembly
- HMMER2 Tools
- HMMER3 Tools
- 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: Mapping Reads
- NGS: RNA-Seq Analysis
- NGS: Variant Analysis
- 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
- Workflow Samples
- Alignment
- Conversions
- Custom Elements
- Data Marking
- Data Merging
- HMMER
- 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 Assembly of 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 Unmapped Reads
- Sanger Sequencing
- Scenarios
- Transcriptomics
- Query Designer
- About the Query Designer
- Query Designer Introduction
- Manipulating Query Designer Element
- Manipulating Schema
- Running Schema from the Sequence View
- Query Designer Schema File Format
- 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
- Algorithm Elements
- Extensions
- DNA Annotator
- DNA Flexibility
- DNA Statistics
- DNA Generator
- ORF Marker
- Remote BLAST
- BLAST
- Repeat Finder
- Restriction Analysis
- Molecular Cloning in silico
- In Silico PCR
- PCR Primer Design for DNA Assembly
- Secondary Structure Prediction
- SITECON
- Smith-Waterman Search
- HMM2
- HMM3
- uMUSCLE
- ClustalW
- MAFFT
- T-Coffee
- Bowtie
- Bowtie 2
- BWA
- BWA-SW
- BWA-MEM
- UGENE Genome Aligner
- CAP3
- SPAdes
- Weight Matrix
- Primer3
- Spliced Alignment mRNA and cDNA
- External Tools Plugin
- ClustalO
- Kalign Aligning
- GeneCut Desktop
- mfold
- UGENE Command Line Interface
- CLI Options
- CLI Predefined Tasks
- Format Converting Sequences
- Converting MSA
- Extracting Sequence
- Finding ORFs
- Finding Repeats
- Finding Patterns Using the 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
- APPENDICES