In this video, we consider the innovations that have appeared in versions 36, 37 and 38. Over the past three versions, Multiple Alignment Editor has had the most part of the improvements.

We continue to inform you about improvements in UGENE versions 33, 34, and 35. In this video, we consider major changes in the Alignment Editor and Sequence View.

Here we briefly introduce you into major features and improvements in UGENE versions 33, 34, and 35. In the first part, we consider the improved mechanism of “External tools” importing, and their integration into the Workflow Designer.

From this video you’ll get a brief overview of new tools and workflows appeared in UGENE versions 1.31 & 1.32 for taxonomic classification of whole-genome Next-Generation Sequencing metagenomic data:

• Integrated tools: Kraken, CLARK, DIAMOND, WEVOTE, MetaPhlAn2
• New sample workflows with the tools
• Results overview

The following updates are described:

• A new mode for editing a sequence
• A new mode for visualizing amino acid translation of a selected region only
• A new easy way to modify a region selection in the Sequence View and Alignment Editor
• Support of Vector NTI/AlignX format

A new framework for analysis of Sanger sequencing reads is described:

• Reads mapping to a reference sequence
• Browsing of the result alignment with trace chromatograms
• Editing the alignment
• Exporting of the results

The following updates are described:

• Extracting a region in the Assembly Browser to a new file
• Support of IUPAC degenerate base symbols when simulating in silico PCR
• Sequence View improvements: editing annotations, translation frames visibility
• New online installer UGENE package that support auto-updating

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

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

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

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

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.

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.

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: Shared Databases 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

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"

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)

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.

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

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.