All Podcast Episodes
UGENE video podcast series teaches you to work with UGENE and answers popular users questions. To stay tuned, subscribe the YouTube channel. Leave your comments on videos or post a request at our forum and watch the answer to your question in video!
#49: What's new in UGENE 1.18&1.19?
Important changes in this major releases include:
- Sequence View: Visibility of the Sequence View subviews (Overview, Zoom View, Details View) can be configured using new buttons on the Sequence View toolbar.
- Multiple Alignments: A region of an alignment can now be copied in the RichText (HTML) format.
- NGS: The SPAdes de novo assembler was updated to 3.6.0 version.
- Usability: Ctrl+V in the Project View was supported. Pasting of data into UGENE was further improved. In particular, you can now paste file using its URL.
- In silico PCR: a possibility to include annotations to the extracted PCR product was added.
- Sequence View: exporting of a sequence image was improved. It is now possible to export the Details View and the Zoom View separately in different formats, including SVG.
- Optimizations of big data processing in UGENE.
UGENE podcast: episode #49 on YouTube
#48: What's new in UGENE 1.17?
Important changes in this major release include:
- Sequence View: recalculation of regions in qualifiers after sequence editing
-
Alignment Editor:
- Aligning of sequences to an existent alignment
- Exporting of multiple alignments to SVG format
- Copying of an alignment region in a chosen format (Ctrl+Shift+C)
- New workflow: In silico PCR
- New workflow: Searching for annotations intersections
- Usability: options panel resizing
UGENE podcast: episode #48 on YouTube
#47: What's new in UGENE 1.16?
Important changes in this major release include:
• Advanced and comfortable search in a project
• Usability:
– Sequence Viewer resizing
– Regrouping of the Tools menu items
– Workflow Designer: generating of output file names
• Sanger reads quality control and alignment
• NGS:
– Reads quality control with FastQC
– Variations annotation with SnpEff
• Alignment Viewer: conservation level highlighting
• Vector NTI sequence format
UGENE podcast: episode #47 on YouTube
#46: What's new in UGENE 1.15?
Important changes in this major release include:
• Quick search in a sequence without creation of annotations
• PCR in silico
• NGS:
– Spades de novo assembler
– Export of a short reads assembly coverage
– Raw NGS filtering workflow samples
– Circular View and circular sequences:
– Support of all algorithms for circular sequences: ORF, restriction sites, BLAST, etc.
– Circular View visualisation settings
• Shared database:
– Support of shared databases in the UGENE Workflow Designer
• Usability improvements:
– Welcome page
– Remembering of Options Panel setting within one
UGENE podcast: episode #46 on YouTube
#45: Phylogenetic trees algorithms
This episode is about phylogenetic trees building methods available in the UGENE platform.
UGENE podcast: episode #45 on YouTube
#44: Overview in the Alignment Editor
This episode will show you how to use the overview of the UGENE Alignment Editor. The overview is the quite powerful feature because it helps with making many things simpler.
By default, the overview repeats the consensus graph on the top of the window, but it shows the whole view of the graph. Using the overview, you can see the regions of an alignment, where sequences are different, and easily navigate to these regions.
UGENE podcast: episode #44 on YouTube
#43: What's new in UGENE 1.14?
Important changes in this major release include:
-
Help system:
- Help buttons were added into all UGENE dialogs.
- The documentation was moved to the Atlassian Confluence system, this makes it easier to search for required information in it.
- Shared storage: sharing of bioinformatics data in a lab. For details, see this page.
-
Alignment Editor:
- Overview for a multiple alignment was added, a lot of configuration options are available.
- A multiple alignment consensus can now be exported.
-
Phylogenetic Trees:
- PhyML Maximum Likelihood was integrated.
- It is now possible to re-root a tree.
- Circular View and circular sequences: a possibility to mark a nucleotide sequence as circular was added. This mark affects how a pattern is searched in the sequence – results located over the end-start junction of it are also found.
- Plasmid features: auto-annotation of the plasmid features like promoters, regulatory regions, primers, etc.
- Export images: exporting of images was improved (multiple alignments, circular molecules, etc.)
-
NGS:
- BWA-MEM tool for aligning short reads was integrated. The tool is available in the GUI dialog and in the Workflow Designer.
- Different workflow elements for sorting, merging and filtering and trimming of NGS data were added (BAM and FASTQ files).
- UGENE Public Storage: the storage can be remotely accessed from any UGENE instance. It contains common genomes and hundreds of plasmids.
- A splash screen was added on the UGENE startup.
UGENE podcast: episode #43 on YouTube
#42: Sharing of bioinformatics data with UGENE
The video gives an introduction to the shared database feature in UGENE.
The database can be used e.g. by colleagues in a lab to share and synchronize different bioinformatics objects (sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, etc.)
When NGS assemblies are shared, only required part of them is loaded to a client computer. That saves time of the researcher and the hard disk space on the client's computer.
The video also mentions the UGENE public storage feature. The storage is opened for read-only access and contains commonly used data (DNA genomes and plasmids).
See also: Shared Databases in UGENE
#41: NGS pipelines in UGENE
A brief overview of NGS pipelines in UGENE: "Variant Calling with SAMtools", "RNA-seq Analysis with Tuxedo", and "ChIP-seq Analysis with Cistrome".
An infrastructure that helps a user to configure the pipelines and investigate the results is also briefly shown: wizards, dashboards, etc.
You should download the NGS package to have the pipelines to be configured out-of-the-box.
Pipelines availability on different OS:
– Windows: SAMtools, Cistrome
– Mac OS X: SAMtools, Tuxedo, Cistrome
– Linux: SAMtools, Tuxedo, Cistrome
#40: What's new in UGENE 1.13?
Important changes in this major release include:
- DAS: you can now annotate an unknown amino acid sequence using annotations of its homologs. First, you search for homologs using the Uniprot BLAST. Second, you load the annotations of the selected homologs to your sequence using the Distributed Annotation System (DAS).
- NCBI Genbank search interface: search for DNA and protein sequences in the GenBank database directly from UGENE.
- Bowtie2: use sequencing reads aligner "Bowtie2" from UGENE GUI.
- Codon table: a new help view "Codon table" was added into the Sequence View. Click "Ctrl+T" to open it there.
- Multiple Alignment Format: a new format PHYLIP is now supported.
- Assembly Format: ACE format is now opened in the Assembly Browser.
- NGS pipelines: "Call variant with SAMtools" pipeline was optimized.
-
Workflow Designer: there were a lot of major and minor improvements.
- Usage of a common workflow output directory
- Storing history of a workflow execution (in dashboards)
- Managing of different workflows output
- Re-running of a workflow from a dashboard
- Debugging of a workflow execution and investigation of an intermediate data state.
- "Workflow schemas" were renamed to "workflows"
#39: What's new in UGENE 1.12?
The latest UGENE 1.12 version is a major release that provides dozens of new features (major and minor), bug fixes and a set of usability and other improvements.
Short list of major features:
- The new entity 'Datasets' in the Workflow Designer which replaces URL parameters
- The MSA editor has been upgraded with pairwise alignment algorithms and the sequence highlighting
- The Assembly Browser allows exporting consensus variations in VCF4 and Simple SNP formats
- Integration with BioMart: extensions for WEB-browsers (Mozilla Firefox and Google Chrome)
#38: What's new in UGENE 1.11?
The latest UGENE 1.11 version is a major release that provides dozens of new features (major and minor), bug fixes and a set of usability and other improvements.
Short list of major features:
- The Sequence View was extended with an options panel
- A consensus sequence for assembly data in the Assembly Browser was added.
- New data flow elements Grouper and Multiplexer in the Workflow Designer were added.
- An mRNA-to-genomic alignment program Spidey was embedded into UGENE as an external tool.
- UGENE 64-bit version is now available for Windows.
#37: What's new in UGENE 1.10?
The latest major UGENE 1.10 release introduces a lot of new features, brings stability, performance and usability improvements into UGENE.
Short list of features and improvements:
- New tools: MrBayes, BWA (all platforms)
- Update of Bowtie and BLAST tools
- Short reads assembly viewer: performance and reads coloring improvements
- Open, view and annotate huge DNA files on a usual desktop
- Workflow Designer: new data filtering elements
- Sequence viewer: new DNA Flexibility and GC Frame Plot graphs
- All in one package: download UGENE, documentation and external tools in a single file
#36: Browsing BAM files with UGENE Assembly Browser
What does the future hold for browsing and analysis of assembly data? This video shows how to use UGENE Assembly Browser – an innovative and fast tool for working with NGS data.
#35: Query Designer working basics
This video covers the UGENE Query Designer working basics.
Learn how to combine different algorithms work and search for complex patterns on a sequence using UGENE Query Designer.
#34: What's new in UGENE 1.9?
This episode starts a new season of UGENE podcast series devoted to the brand new UGENE release. In this video you will find an overview of the multiple new UGENE features including such significant ones as
- Cloning "in silico" support capabilities,
- Query Designer complex sequence analysis tool,
- A new human-readable schema format and language
- and more.
In the next episodes all the new features will be covered in detail.
We hope you will enjoy UGENE 1.9 and the video tutorials.
#33: Performing BLAST search and FormatDB database construction with UGENE
Performing BLAST search and constructing custom BLAST database is available from UGENE with the External Tool Support plugin. Watch this video to find out how to do so and how to use the Workflow Designer „Local BLAST search" element.
#32: What's new in UGENE 1.8?
Find out about the new UGENE 1.8 features and enhancements in this video! In version 1.8.0 UGENE team concentrated efforts on the stability and reliability of the project, which resulted in over than 100 bugfixes implemented. New features:
- Support for external Blast: FormatDB and search;
- Workflow Designer and command-line UGENE enhancements;
- New format is supported: MEGA;
- Support for large (over 1 GB) files analysis in DNA Assembly;
- The plugin API is invented (developers-level).
#31: Custom scripts in Workflow Designer
Getting back to the innovative UGENE Workflow Designer. A number of element attributes (parameters) can be calculated in a script on basis of other element attributes values. Take a look at the working example!
#30: Primer design in UGENE
The video provides an introduction into primer design in UGENE.
#29: What's new in UGENE 1.7.2?
New UGENE version 1.7.2 allows you to :
- use external tools within UGENE,
- develop your own processes in Workflow Designer,
- use the enhanced Dotplot,
- download UGENE manual and work with the NEXUS file format.
Also this version of UGENE contains an important innovation into UGENE distributed computing system. Watch these videos to know more of these new features.
#28: Using Dotplot to compare sequences
Dotplot allows the graphical comparison of two biological sequences with identifying the regions of similarity. In this video you will find an example of sequence comparison with UGENE Dotplot plugin with the analysis of features of the plot.
#27: Finding tandem repeats in a DNA sequence in UGENE
UGENE provides a fast and memory efficient way to search for tandem repeats. You can use it for pedigree determination or for other purposes.
#26: Using bookmarks to save and restore views states in UGENE
In UGENE you can save and restore object views states using the bookmark mechanism. In this episode we work with object views and use bookmarks to save any adjustments that we made to a view.
#25: What's new in UGENE 1.7.1?
Welcome to the next "What's new in UGENE?" video dedicated to the UGENE version 1.7.1 release!
The new features include:
- Dotplot plugin for sequence visualization and comparison
- Advanced chromatogram analysis
- SAM and Phred DNA quality scores file formats support
- New DNA Assembly Workflow Designer schemas, console commands and plugin options
- Batch processing for weight matrices
- Restriction enzymes improvements (circular option)
- Smith-Waterman algorithm optimization for using with GPU's
#24: SITECON: Searching for TFBS and making TFBS alignments profiles
UGENE SITECON plugin is a program package for searching for potential transcription factor binding sites. The tool is developed in Institute of Cytology and Genetics SB RAS.
The video shows how to use SITECON to search for TFBS in a DNA sequence and how to create SITECON profiles for future searches.
#23: Searching for homologs of protein sequence with HMMER3
Today's topic is using HMMER3 tools from UGENE. The UGENE version is intended to provide a wider user audience with a high-performance HMMER-compatible solution. Here's the tutorial.
#22: Creating custom console command (MUSCLE alignment with various output format)
The tutorial shows how to easily create custom console command in UGENE and then use it.
#21: Searching for transcription binding sites with UGENE Weight Matrix plugin
Today we consider the new Weight Matrix plugin which allows to search for transcription factor binding sites and to create and save position weight and frequency matrices.
#20: What's new in UGENE 1.7? Part 2/2
In the second part we consider the new plugins that have been added to UGENE: DNA Assembly plugin, Weight Matrix plugin and Query remote database plugin, and the support of GFF format.
#19: What's new in UGENE 1.7? Part 1/2
The second „What's new in UGENE? video dedicated to the UGENE version 1.7 release. The video goes in two parts. In the first part we consider significant Circular View enhancements, the added Overview, new powerful command line interface and the added scripting framework.
#18: Performing profile-to-profile and profile-to-sequence MUSCLE alignments
Besides making multiple sequence alignments with MUSCLE and KAling, UGENE users can align two already existing alignments of related sequences, which is also called „profile-profile alignment. Also it is possible to align a set of sequences to a MUSCLE profile in UGENE. Today we consider these use cases.
#17: Finding repeats in a DNA sequence in UGENE
Today we will search for repeats in a DNA sequence in UGENE. There's a set of the search options to set, and we consider them all in this episode.
#16: Using UGENE as chromatograms viewer and editor
UGENE makes it possible to visualize a chromatogram and to edit a sequence being guided by a chromatogram. How to do this exactly? It's all in the video.
#15: Working with Open Reading Frames (ORFs) in UGENE
This episode is about searching for ORFs with UGENE. All the search options are considered and explained.
#14: What's new in UGENE 1.6.2?
Today we have a special episode. We will to talk about what's new in the latest UGENE release: version 1.6.2, which was released this week.
#13: Working with large alignments in UGENE
Today we will discuss how to work with large sequence alignment with MUSCLE and KAlign UGENE plugins, including alignments containing more than 100,000 sequences.
#12: Searching restriction enzymes cut sites with UGENE
In UGENE you can search for restriction enzymes cut sites in a DNA sequence. Today we will use Restriction Enzymes plugin to perform such a search.
#11: 3D Structure Viewer, part 2: image export, multiple structure view
We continue working with 3D Structure Viewer plugin which visualizes 3D structures from files of PDB and MMDB formats.
#10: Using Workflow Designer to export sequences from PDB files into FASTA files
In UGENE you can create and run complex computational workflows. Today we will perform exporting hundred of sequences from PDB files into new FASTA files, using UGENE Workflow Designer, a flexible and and intuitive measuring tool.
#9: Performing local sequence alignment with Smith-Waterman algorithm
Today we will use Smith-Waterman algorithm to perform a local sequence alignment, which means determining similar regions between two nucleotide or protein sequences.
#8: 3D Structure viewer, part 1: basic operations
In this episode we will see how UGENE works with data formats containing 3D macromolecular structure, such as PDB or MMDB.
#7: Querying remote database
Where to get the data to work with in UGENE? A considerable choice is remote databases containing large amounts of sequences, alignments, 3d structures e.t.c. In this episode we will work with remote databases.
#6: Running remote MUSCLE task
UGENE provides a way of performing distributed computing. It's implemented with remote task mechanism. You can perform a task on a machine that runs UGENE and are available from local network or in the Internet.
#5: Working with annotations, part 2: using qualifiers
This time we dwell into annotations, add some qualifiers to annotations and see how annotations could be sorted by the qualifiers values here in UGENE.
#4: Working with annotations, part 1: creating annotations
In the 4th episode you will see how to work with annotations here in UGENE. Also the video tells of how to save separate files and the whole project, including associations between files.
#3: Working with multiple sequence alignment, the basics
What does Multiple Sequence Alignment look like here in UGENE? What could it do? We learn that in the third UGENE podcast episode.
#2: Working with a sequence: basic operations part 1
In the second episode we work further with sequences in UGENE, a free cross-platform genome analysis suite. We open GenBank file, look at the annotations and find out what's all this stuff on the screen.
#1: Making a multiple sequence alignment from FASTA file
In this episode you'll learn the basic stuff of working with FASTA sequence containers and making multiple sequence alignments.