Uploads by UniproUGENE

UGENE podcast #38: Whats new in UGENE 1.11

UniproUGENE — Sat, 26 May 2012 11:21:30 +0000

	UGENE podcast #38: Whats 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. The major changes are: * The Sequence View was extended with an options panel. It shows interactive information about a selected sequence region, allows you to easily set up the annotation types' properties (for example annotations' colors) and to search for a pattern in a sequence. * You can now calculate a consensus sequence for assembly data in the Assembly Browser, using either a simple default algorithm or an algorithm from SAMtools. Also, it is now possible to highlight paired reads and SNP in assembly data. Another minor handy feature is the possibility to add bookmarks in the Assembly Browser. * To create more sophisticated workflows in the Workflow Designer you can use new data flow elements Grouper and Multiplexer. * An mRNA-to-genomic alignment program Spidey was embedded into UGENE as an external tool. * UGENE 64-bit version is now available for Windows.	From: UniproUGENE Views: 27 3 ratings
	Time: 05:05	More in Science & Technology

UGENE podcast #37: Whats new in UGENE 1.10

UniproUGENE — Mon, 05 Dec 2011 11:45:02 +0000

	UGENE podcast #37: Whats new in UGENE 1.10 Find out about the new UGENE 1.10 features and enhancements in this video! Download UGENE: ugene.unipro.ru 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	From: UniproUGENE Views: 617 1 ratings
	Time: 04:37	More in Science & Technology

UGENE podcast #32: What's new in UGENE 1.8?

UniproUGENE — Sun, 04 Dec 2011 11:41:09 +0000

	UGENE podcast #32: What's new in UGENE 1.8? Find out about the new UGENE 1.8 features and enhancements in this video! Download new UGENE right here! ugene.unipro.ru 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).	From: UniproUGENE Views: 33 0 ratings
	Time: 04:13	More in Science & Technology

UGENE podcast #36: Browsing BAM files with UGENE Assembly Browser

UniproUGENE — Mon, 24 Oct 2011 09:13:13 +0000

	UGENE podcast #36: Browsing BAM files with UGENE Assembly Browser What does the future hold for browsing and analysis of assembly data? This video will show you how to use UGENE Assembly Browser - an innovative and fast tool for working with NGS data.	From: UniproUGENE Views: 504 1 ratings
	Time: 05:28	More in Science & Technology

UGENE podcast #35: Query Designer working basics

UniproUGENE — Fri, 07 Jan 2011 15:12:03 +0000

	UGENE podcast #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.	From: UniproUGENE Views: 615 3 ratings
	Time: 06:57	More in Science & Technology

UGENE podcast #34: What's new in UGENE 1.9?

UniproUGENE — Fri, 17 Dec 2010 16:40:55 +0000

	UGENE podcast #34: What's new in UGENE 1.9? 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, so feel free to subscribe.	From: UniproUGENE Views: 483 5 ratings
	Time: 08:58	More in Science & Technology

UGENE podcast #33: Performing BLAST search and FormatDB database construction with UGENE

UniproUGENE — Thu, 21 Oct 2010 15:32:08 +0000

	UGENE podcast #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" worker.	From: UniproUGENE Views: 618 2 ratings
	Time: 04:16	More in Science & Technology

UGENE podcast #32: What's new in UGENE 1.8?

UniproUGENE — Thu, 21 Oct 2010 15:23:31 +0000

	UGENE podcast #32: What's new in UGENE 1.8? Find out about the new UGENE 1.8 features and enhancements in this video! Download new UGENE right here! ugene.unipro.ru 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).	From: UniproUGENE Views: 123 1 ratings
	Time: 04:13	More in Science & Technology

UGENE podcast #31: Using attribute scripts in Workflow Designer

UniproUGENE — Thu, 21 Oct 2010 15:03:29 +0000

	UGENE podcast #31: Using attribute scripts in Workflow Designer Getting back to the innovative UGENE Workflow Designer. A number of worker attributes (parameters) can be calculated in a script on basis of other worker attributes values. Take a look at the working exapmle!	From: UniproUGENE Views: 111 0 ratings
	Time: 03:59	More in Science & Technology

UGENE podcast #30: Primer Design in UGENE

UniproUGENE — Wed, 08 Sep 2010 15:48:40 +0000

	UGENE podcast #30: Primer Design in UGENE The video provides an introduction into primer desing in UGENE.	From: UniproUGENE Views: 519 0 ratings
	Time: 03:20	More in Science & Technology

UGENE podcast #29: What's new in UGENE 1.7.2? Part 2

UniproUGENE — Sat, 21 Aug 2010 02:00:40 +0000

	UGENE podcast #29: What's new in UGENE 1.7.2? Part 2 UGENE now supports cloud computing. Unipro company is capable of installing and maintaining UGENE distributed computation service in any private local network or cluster environment. Please contact us for details: ugene@unipro.ru	From: UniproUGENE Views: 79 0 ratings
	Time: 02:27	More in Science & Technology

UGENE podcast #29: What's new in UGENE 1.7.2? Part 1

UniproUGENE — Sat, 21 Aug 2010 01:40:35 +0000

	UGENE podcast #29: What's new in UGENE 1.7.2? Part 1 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 this video to know more of these new features.	From: UniproUGENE Views: 183 0 ratings
	Time: 08:37	More in Science & Technology

UGENE podcast #28: Using Dotplot to compare sequences

UniproUGENE — Thu, 12 Aug 2010 06:28:02 +0000

	UGENE podcast #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.	From: UniproUGENE Views: 305 0 ratings
	Time: 07:13	More in Science & Technology

UGENE podcast #27: Finding tandem repeats in a DNA sequence in UGENE

UniproUGENE — Mon, 19 Jul 2010 15:45:04 +0000

	UGENE podcast #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. Watch the episode for details.	From: UniproUGENE Views: 418 1 ratings
	Time: 02:47	More in Science & Technology

UGENE podcast #26: Using bookmarks to save and restore views states in UGENE

UniproUGENE — Wed, 14 Jul 2010 16:42:46 +0000

	UGENE podcast #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.	From: UniproUGENE Views: 63 0 ratings
	Time: 04:00	More in Science & Technology

UGENE podcast #25: What's new in UGENE 1.7.1?

UniproUGENE — Tue, 13 Jul 2010 08:38:23 +0000

	UGENE podcast #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	From: UniproUGENE Views: 180 1 ratings
	Time: 07:36	More in Science & Technology

UGENE podcast, episode #24: SITECON: Searching for TFBS and making TBFS alignments profiles

UniproUGENE — Mon, 28 Jun 2010 16:36:50 +0000

	UGENE podcast, episode #24: SITECON: Searching for TFBS and making TBFS 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.	From: UniproUGENE Views: 107 0 ratings
	Time: 04:06	More in Science & Technology

UGENE podcast, episode #23: Searching for homologs of protein sequence with HMMMER3

UniproUGENE — Wed, 23 Jun 2010 11:53:29 +0000

	UGENE podcast, episode #23: Searching for homologs of protein sequence with HMMMER3 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.	From: UniproUGENE Views: 305 0 ratings
	Time: 05:36	More in Science & Technology

UGENE podcast #22: Creating custom console command (MUSCLE alignment with various output format)

UniproUGENE — Thu, 10 Jun 2010 12:26:28 +0000

	UGENE podcast #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.	From: UniproUGENE Views: 150 1 ratings
	Time: 04:07	More in Science & Technology

UGENE podcast #21: Searching for transcription binding sites with UGENE Weight Matrix plugin

UniproUGENE — Wed, 02 Jun 2010 14:41:03 +0000

	UGENE podcast #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.	From: UniproUGENE Views: 216 0 ratings
	Time: 04:31	More in Science & Technology

UGENE podcast #20: What's new in UGENE 1.7? Part 2/2.

UniproUGENE — Sun, 23 May 2010 11:59:55 +0000

	UGENE podcast #20: What's new in UGENE 1.7? Part 2/2. The second „What's new in UGENE? video dedicated to the UGENE version 1.7 release. The video goes in two parts. In the 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.	From: UniproUGENE Views: 161 0 ratings
	Time: 06:20	More in Science & Technology

UGENE podcast #19: What's new in UGENE 1.7? Part 1/2.

UniproUGENE — Sun, 23 May 2010 11:55:06 +0000

	UGENE podcast #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.	From: UniproUGENE Views: 146 0 ratings
	Time: 05:39	More in Science & Technology

UGENE podcast #18: Performing profile-to-profile and profile-to-sequence MUSCLE alignments

UniproUGENE — Thu, 29 Apr 2010 14:03:18 +0000

	UGENE podcast #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.	From: UniproUGENE Views: 373 1 ratings
	Time: 04:00	More in Science & Technology

UGENE podcast #17: Finding repeats in a DNA sequence in UGENE

UniproUGENE — Mon, 19 Apr 2010 09:09:41 +0000

	UGENE podcast #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.	From: UniproUGENE Views: 343 0 ratings
	Time: 03:45	More in Science & Technology

UGENE podcast #16: Using UGENE as chromatograms viewer and editor

UniproUGENE — Wed, 07 Apr 2010 20:49:18 +0000

	UGENE podcast #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.	From: UniproUGENE Views: 399 0 ratings
	Time: 03:18	More in Science & Technology