Fedora 19 Update: ugene-1.13.0-1.fc19

[updates at fedoraproject.org]

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Fedora Update Notification
FEDORA-2013-23280
2013-12-13 03:52:52
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Name        : ugene
Product     : Fedora 19
Version     : 1.13.0
Release     : 1.fc19
URL         : http://ugene.unipro.ru
Summary     : Integrated bioinformatics toolkit
Description :
Unipro UGENE is a cross-platform visual environment for DNA and protein
sequence analysis. UGENE integrates the most important bioinformatics
computational algorithms and provides an easy-to-use GUI for performing
complex analysis of the genomic data. One of the main features of UGENE
is a designer for custom bioinformatics workflows.

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Update Information:

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"

See the release podcast episode for details about the features (https://www.youtube.com/watch?v=iuT-KOSpB6U).

The full list of the new features, improvements and bug fixes can be found in our bug tracker (https://ugene.unipro.ru/tracker/browse/UGENE-2533?jql=project%20%3D%20UGENE%20AND%20fixVersion%20%3D%20%221.13%22%20AND%20resolution%20is%20not%20EMPTY).
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ChangeLog:

* Wed Dec 11 2013 Yulia Algaer <yalgaer at unipro.ru> 1.13.0-1
- Upstream version change
* Wed Oct  9 2013 Yulia Algaer <yalgaer at unipro.ru> 1.12.3-1
- Upstream version change
* Tue Aug 20 2013 Yulia Algaer <yalgaer at unipro.ru> 1.12.2-1
- Upstream version change
* Thu Aug  8 2013 Yulia Algaer <yalgaer at unipro.ru> 1.12.1-1
- Upstream version change
* Fri Jun 28 2013 Yulia Algaer <yalgaer at unipro.ru> 1.12.0-1
- Upstream version change
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This update can be installed with the "yum" update program.  Use 
su -c 'yum update ugene' at the command line.
For more information, refer to "Managing Software with yum",
available at http://docs.fedoraproject.org/yum/.

All packages are signed with the Fedora Project GPG key.  More details on the
GPG keys used by the Fedora Project can be found at
https://fedoraproject.org/keys
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