Contents :: About Unipro »
Contents¶
- Basic Functions
- UGENE Terminology
- UGENE Window Components
- Main Menu Overview
- Creating New Project
- Opening Document
- Creating Document
- Locked Documents
- Using Objects and Object Views
- Using Bookmarks
- Working with Projects
- Adding and Removing Plugins
- Fetching Data from Remote Database
- UGENE Application Settings
- Creating and Using Index File
- Sequence View
- Sequence View Extensions
- Circular Viewer
- 3D Structure Viewer
- Chromatogram Viewer
- DNA Graphs Package
- Dotplot
- Alignment Editor
- Assembly Browser
- Phylogenetic Tree Viewer
- Distributed Computing
- Plugins
- Workflow Designer
- DNA Annotator
- DNA Flexibility
- DNA Export
- DNA Statistics
- ORF Marker
- Remote BLAST
- Repeat Finder
- Restriction Analysis
- Molecular Cloning in silico
- Secondary Structure Prediction
- SITECON
- Smith-Waterman Search
- HMM2
- HMM3
- uMUSCLE
- Bowtie
- BWA
- UGENE Genome Aligner
- CAP3
- Weight Matrix
- Primer3
- External Tools
- Query Designer
- UGENE Command Line Interface
- CLI Options
- CLI Predefined Tasks
- 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 Bowtie Index
- Aligning Short Reads with Bowtie
- Building Profile HMM Using HMMER2
- Searching HMM Signals Using HMMER2
- Aligning with ClustalW
- Aligning with Kalign
- Aligning with MAFFT
- Aligning with MUSCLE
- 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
- Creating Custom CLI Tasks
- APPENDICES