UGENE

UGENE

A dark blue, nearly square rectangle, within which is a light grey, sans-serif, capital letter U.

UGENE logo
Original author(s) Okonechnikov K., Golosova O.
Developer(s) Unipro
Initial release 2008 (2008)
Stable release
1.25.0 / 7 October 2016 (2016-10-07)
Development status Active
Written in C++, Qt
Operating system Cross-platform: Windows, macOS, Linux
Available in English, Russian
Type Bioinformatics toolkit
License GPLv2
Website ugene.net

UGENE is computer software for bioinformatics.[1][2] It works on desktop computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.

UGENE helps biologists to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. The data can be stored both locally (on a personal computer) and on a shared storage (e.g., a lab database).

UGENE integrates dozens of well-known biological tools, algorithms, and original tools in the context of genomics, evolutionary biology, virology, and other branches of life science. UGENE provides a graphical user interface (GUI) for the pre-built tools so biologists with no computer programming skills can access those tools more easily.

Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data readers, blocks executing embedded tools and algorithms, and data writers. Blocks can be created with command line tools or a script. A set of sample workflows is available in the Workflow Designer, to annotate sequences, convert data formats, analyze NGS data, etc.

Beside the graphical interface, UGENE also has a command-line interface. Workflows may also be executed thereby.

To improve performance, UGENE uses multi-core processors (CPUs) and graphics processing units (GPUs) to optimize a few algorithms.[3][4]

Key features

The software supports the following features:

Sequence View

The Sequence View is used to visualize, analyze and modify nucleic acid or protein sequences. Depending on the sequence type and the options selected, the following views can be present in the Sequence View window:

Alignment Editor

The Alignment Editor allows working with multiple nucleic acid or protein sequences - aligning them, editing the alignment, analyzing it, storing the consensus sequence, building a phylogenetic tree, and so on.

Phylogenetic Tree Viewer

The Phylogenetic Tree Viewer helps to visualize and edit phylogenetic trees. It is possible to synchronize a tree with the corresponding multiple alignment used to build the tree.

Assembly Browser

Assembly Browser

The Assembly Browser project was started in 2010 as an entry for Illumina iDEA Challenge 2011.[19] The browser allows users to visualize and browse large (up to hundreds of millions of short reads) next generation sequence assemblies. It supports SAM,[20] BAM (the binary version of SAM), and ACE formats. Before browsing assembly data in UGENE, an input file is converted to a UGENE database file automatically. This approach has its pros and cons. The pros are that this allows viewing the whole assembly, navigating in it, and going to well-covered regions rapidly. The cons are that a conversion may take time for a large file, and needs enough disk space to store the database.

Workflow Designer

UGENE Workflow Designer allows creating and running complex computational workflow schemas.[21]

The distinguishing feature of Workflow Designer, relative to other bioinformatics workflow management systems is that workflows are executed on a local computer. It helps to avoid data transfer issues, whereas other tools’ reliance on remote file storage and internet connectivity does not.

The elements that a workflow consists of correspond to the bulk of algorithms integrated into UGENE. Using Workflow Designer also allows creating custom workflow elements. The elements can be based on a command-line tool or a script.

Workflows are stored in a special text format. This allows their reuse, and transfer between users.

A workflow can be run using the graphical interface or launched from the command line. The graphical interface also allows controlling the workflow execution, storing the parameters, and so on.

There is an embedded library of workflow samples to convert, filter, and annotate data, with several pipelines to analyze NGS data developed in collaboration with NIH NIAID.[22] A wizard is available for each workflow sample.

Supported biological data formats

Release cycle

UGENE is primarily developed by Unipro LLC[23] with headquarters in Akademgorodok of Novosibirsk, Russia. Each iteration lasts about 1–2 months, followed by a new release. Development snapshots may also be downloaded.

The features to include in each release are mostly initiated by users.

See also

References

  1. ↑ Okonechnikov K, Golosova O, Fursov M, the UGENE team (2012). "Unipro UGENE: a unified bioinformatics toolkit". Bioinformatics. 28 (8): 1166–7. doi:10.1093/bioinformatics/bts091. PMID 22368248.
  2. ↑ Fursov, M.; Novikova, O. (2008). "Multitasking software system for DNA analysis" (PDF). Proceedings of the Sixth International Conference on Bioinformatics of Genome Regulation and Structure. 1: 78. ISBN 978-5-91291-005-0.
  3. ↑ Fursov, M. Y.; Oshchepkov, D. Y; Novikova, O. S. (2009). "UGENE: interactive computational schemes for genome analysis" (PDF). Proceedings of the Fifth Moscow International Congress on Biotechnology. 3: 14–15. ISBN 5-7237-0372-2.
  4. ↑ Efremov, I. E.; Fursov, M. Y; Danilova, Yu. E. (2009). "UGENE: high performance genome analysis suite". Proceedings of the Fifth Moscow International Congress on Biotechnology. 2: 405–406. ISBN 5-7237-0372-2.
  5. ↑ REBASE
  6. ↑ Primer3
  7. ↑ BWA
  8. ↑ SAMtools
  9. ↑ TopHat
  10. ↑ Cufflinks
  11. ↑ MACS
  12. ↑ CEAS
  13. ↑ MrBayes
  14. ↑ PhyML
  15. ↑ CAP3
  16. 1 2 Molecular Modeling Database (MMDB)
  17. ↑ Spidey
  18. ↑ Vaskin, Y.; Khomicheva, I.; Ignatieva, E.; Vityaev, E. (2012). "ExpertDiscovery and UGENE integrated system for intelligent analysis of regulatory regions of genes". In Silico Biology. 11 (3-4): 97–108. doi:10.3233/ISB-2012-0448. PMID 22935964.
  19. ↑ Illumina iDEA Challenge 2011
  20. ↑ SAM
  21. ↑ Fursov, M. Y.; Varlamov, A. (2009). "UGENE - A practical approach for complex computational analysis in molecular biology" (PDF). Proceedings of the 10th Annual Bioinformatics Open Source Conference: 7.
  22. ↑ NIH NIAID
  23. ↑ Unipro LLC
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