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 or the RSS. Leave your comments on videos or post a request at our forum and watch the answer to your question in video!

Click on a link below to open the detailed description of an episode. Each description contains a link to the YouTube video and a download link. To watch a downloaded video use the QuickTime Player or another player with MPEG4 support.

#37	What's new in UGENE 1.10?
#36	Browsing BAM files with UGENE Assembly Browser
#35	Query Designer working basics
#34	What's new in UGENE 1.9?
#33	Performing BLAST search and FormatDB database construction with UGENE
#32	What's new in UGENE 1.8?
#31	Custom scripts in Workflow Designer
#30	Primer design in UGENE
#29	What's new in UGENE 1.7.2?
#28	Using Dotplot to compare sequences
#27	Finding tandem repeats in a DNA sequence in UGENE
#26	Using bookmarks to save and restore views states in UGENE
#25	What's new in UGENE 1.7.1?
#24	SITECON: Searching for TFBS and making TFBS alignments profiles
#23	Searching for homologs of protein sequence with HMMER3
#22	Creating custom console command (MUSCLE alignment with various output format)
#21	Searching for transcription binding sites with UGENE Weight Matrix plugin
#20	What's new in UGENE 1.7? Part 2/2
#19	What's new in UGENE 1.7? Part 1/2
#18	Performing profile-to-profile and profile-to-sequence MUSCLE alignments
#17	Finding repeats in a DNA sequence in UGENE
#16	Using UGENE as chromatograms viewer and editor
#15	Working with Open Reading Frames (ORFs) in UGENE
#14	What's new in UGENE 1.6.2?
#13	Working with large alignments in UGENE
#12	Searching restriction enzymes cut sites with UGENE
#11	3D Structure Viewer, part 2: image export, multiple structure view
#10	Using Workflow Designer to export sequences from PDB files into FASTA files
#9	Performing local sequence alignment with Smith-Waterman algorithm
#8	3D Structure viewer, part 1: basic operations
#7	Querying remote database
#6	Running remote MUSCLE task
#5	Working with annotations, part 2: using qualifiers
#4	Working with annotations, part 1: creating annotations
#3	Working with multiple sequence alignment, the basics
#2	Working with a sequence: basic operations part 1
#1	Making a multiple sequence alignment from FASTA file

#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 Desginer „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 analisys 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 exapmle!

#30: Primer design in UGENE

The video provides an introduction into primer desing 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
• Restricition 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 Overiew, 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 associatons 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.