Unipro UGENE podcast UGENE podcast is a series of the video product tutorials. It contains useful information of how to work with UGENE and answers the popular users questions. If you would like to see new episodes first, just subscribe the YouTube channel or the RSS. Leave your comments to the videos or post requests at our forum and watch the answer to your question in video!
#27: Finding tandem repeats in a DNA sequence in UGENEUGENE 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 UGENEIn 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:
#24: SITECON: Searching for TFBS and making TFBS alignments profilesUGENE 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 HMMMER3Today'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 pluginToday 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 2/2In 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 1/2The 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 alignmentsBesides 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 UGENEToday 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 editorUGENE 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 UGENEThis 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 UGENEToday 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 UGENEIn 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 viewWe 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 filesIn 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 algorithmToday 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 operationsIn this episode we will see how UGENE works with data formats containing 3D macromolecular structure, such as PDB or MMDB.#7: Querying remote databaseWhere 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 taskUGENE 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 qualifiersThis 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 annotationsIn 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 basicsWhat 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 1In 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 fileIn this episode you'll learn the basic stuff of working with FASTA sequence containers and making multiple sequence alignments. |
