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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.

#49 What's new in UGENE 1.18&1.19?
#48 What's new in UGENE 1.17?
#47 What's new in UGENE 1.16?
#46 What's new in UGENE 1.15?
#45 Phylogenetic trees algorithms
#44 Overview in the Alignment Editor
#43 What's new in UGENE 1.14?
#42 Sharing of bioinformatics data with UGENE
#41 NGS pipelines in UGENE
#40 What's new in UGENE 1.13?
#39 What's new in UGENE 1.12?
#38 What's new in UGENE 1.11?
#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

 

#49: What's new in UGENE 1.18&1.19?

Important changes in this major releases include:

UGENE podcast: episode #49 on YouTube

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#48: What's new in UGENE 1.17?

Important changes in this major release include:

UGENE podcast: episode #48 on YouTube

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#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

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#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

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#45: Phylogenetic trees algorithms

This episode is about phylogenetic trees building methods available in the UGENE platform.

UGENE podcast: episode #45 on YouTube

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#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

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#43: What's new in UGENE 1.14?

Important changes in this major release include:

UGENE podcast: episode #43 on YouTube

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#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 assemlies, 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: http://ugene.unipro.ru/shared-db.html

UGENE podcast: episode #42 on YouTube
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#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 breifly 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

UGENE podcast: episode #41 on YouTube
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#40: What's new in UGENE 1.13?

Important changes in this major release include:

UGENE podcast: episode #40 on YouTube
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#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:

UGENE podcast: episode #39 on YouTube
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#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:

UGENE podcast: episode #38 on YouTube
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#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:

UGENE podcast: episode #37 on YouTube
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#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.

UGENE podcast: episode #36 on YouTube
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Download a zip-archive with an example BAM file and the reference sequence

#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.

UGENE podcast: episode #35 on YouTube
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#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

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.

UGENE podcast: episode #34 on YouTube
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#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.

UGENE podcast: episode #33 on YouTube
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#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:

UGENE podcast: episode #32 on YouTube
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#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!

UGENE podcast: episode #31 on YouTube
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#30: Primer design in UGENE

The video provides an introduction into primer desing in UGENE.

UGENE podcast: episode #30 on YouTube
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#29: What's new in UGENE 1.7.2?

New UGENE version 1.7.2 allows you to :

Also this version of UGENE contains an important innovation into UGENE distributed computing system. Watch these videos to know more of these new features.

UGENE podcast: episode #29 (part 1) on YouTube
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UGENE podcast: episode #29 (part 2) on YouTube
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#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.

UGENE podcast: episode #28 on YouTube
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#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.

UGENE podcast: episode #27 on YouTube
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#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.

UGENE podcast: episode #26 on YouTube
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#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:

UGENE podcast: episode #25 on YouTube
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#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.

UGENE podcast: episode #24 on YouTube
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#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.

UGENE podcast: episode #23 on YouTube
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#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.

UGENE podcast: episode #22 on YouTube
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#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.

UGENE podcast: episode #21 on YouTube
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#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.

UGENE podcast: episode #20 on YouTube
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#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.

UGENE podcast: episode #19 on YouTube
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#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.

UGENE podcast: episode #18 on YouTube
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#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.

UGENE podcast: episode #17 on YouTube
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#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.

UGENE podcast: episode #16 on YouTube
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#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.

UGENE podcast: episode #15 on YouTube
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#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.

UGENE podcast: episode #14 on YouTube
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#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.

UGENE podcast: episode #13 on YouTube
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#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.

UGENE podcast: episode #12 on YouTube
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#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.

UGENE podcast: episode #11 on YouTube
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#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.

UGENE podcast: episode #10 on YouTube
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#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.

UGENE podcast: episode #9 on YouTube
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#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.

UGENE podcast: episode #8 on YouTube
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#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.

UGENE podcast: episode #7 on YouTube
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#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.

UGENE podcast: episode #6 on YouTube
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#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.

UGENE podcast: episode #5 on YouTube
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#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.

UGENE podcast: episode #4 on YouTube
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#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.

UGENE podcast: episode #3 on YouTube
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#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.

UGENE podcast: episode #2 on YouTube
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#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.

UGENE podcast: episode #1 on YouTube
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