Ugene

UGENE
UGENE logo
Original author(s) Fursov M.
Developer(s) Unipro
Initial release 2008
Stable release 41
/ 3 December 2021
Written in C++, Qt
Operating system Windows, macOS, Linux
Available in English, Russian
Type Bioinformatics toolkit
License GPLv2
Website ugene.net (http://ugene.ne
t)
UGENE
UGENE is computer software for bioinformatics.[1][2]
It works on personal 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
Sequence View
Alignment Editor
Phylogenetic Tree Viewer
Assembly Browser
Contents

Workflow Designer
Supported biological data formats
Release cycle
See also
References
External links
The software supports the following features:
Create, edit, and annotate nucleic acid and protein sequences
Fast search in a sequence
Multiple sequence alignment: Clustal W and O, MUSCLE, Kalign, MAFFT, T-Coffee
Create and use shared storage, e.g., lab database
Search through online databases: National Center for Biotechnology Information (NCBI),
Protein Data Bank (PDB), UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, DAS servers
Local and NCBI Genbank BLAST search
Open reading frame finder
Restriction enzyme finder with integrated REBASE[5] restriction enzymes list
Integrated Primer3 package[6] for PCR primer design
Plasmid construction and annotation
Cloning in silico by designing of cloning vectors
Genome mapping of short reads with Bowtie, BWA,[7] and UGENE Genome Aligner
Visualize next generation sequencing data (BAM files) using UGENE Assembly Browser
Variant calling with SAMtools[8]
RNA-Seq data analysis with Tuxedo pipeline (TopHat,[9] Cufflinks,[10] etc.)
ChIP-seq data analysis with Cistrome pipeline (MACS,[11] CEAS,[12] etc.)
Raw NGS data processing
HMMER 2 and 3 packages integration
Chromatogram viewer
Search for transcription factor binding sites (TFBS) with weight matrix and SITECON (http://
wwwmgs.bionet.nsc.ru/cgi-bin/mgs/sitecon/sitecon.pl?stage=0) algorithms
Search for direct, inverted, and tandem repeats in DNA sequences
Local sequence alignment with optimized Smith-Waterman algorithm
Build (using integrated PHYLIP neighbor joining, MrBayes,[13] or PhyML[14] Maximum
Likelihood) and edit phylogenetic trees
Combine various algorithms into custom workflows with UGENE Workflow Designer
Contigs assembly with CAP3[15]
3D structure viewer for files in Protein Data Bank (PDB) and Molecular Modeling Database
(MMDB)[16] formats, anaglyph view support
Predict protein secondary structure with GOR IV and PSIPRED algorithms
Construct dot plots for nucleic acid sequences
mRNA alignment with Spidey[17]
Key features

Assembly Browser
Search for complex signals with ExpertDiscovery[18]
Search for a pattern of various algorithms' results in a nucleic acid sequence with UGENE
Query Designer
PCR in silico for primer designing and mapping
Spade de novo assembler
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:
3D structure view
Circular view
Chromatogram view
Graphs View: GC-content, AG-content, and other
Dot plot view
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.
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.
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.
UGENE Workflow Designer allows creating and running complex computational workflow schemas.[21]
Sequence View
Alignment Editor
Phylogenetic Tree Viewer
Assembly Browser
Workflow Designer

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.
Sequences and annotations: FASTA (.fa), GenBank (.gb), EMBL (.emb), GFF (.gff)
Multiple sequence alignments: Clustal (.aln), MSF (.msf), Stockholm (.sto), Nexus (.nex)
3D structures: PDB (.pdb), MMDB (.prt)[16]
Chromatograms: ABIF (.abi), SCF (.scf)
Short reads: Sequence Alignment/Map(SAM) (.sam), binary version of SAM (.bam), ACE
(.ace), FASTQ (.fastq)
Phylogenetic trees: Newick (.nwk), PHYLIP (.phy)
Other formats: Bairoch (enzymes info), HMM (HMMER profiles), PWM and PFM (position
matrices), SNP and VCF4 (genome variations)
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.
Sequence alignment software
Bioinformatics
Computational biology
List of open source bioinformatics software
1. Okonechnikov K, Golosova O, Fursov M, the UGENE team (2012). "Unipro UGENE: a
unified bioinformatics toolkit" (https://doi.org/10.1093%2Fbioinformatics%2Fbts091).
Supported biological data formats
Release cycle
See also
References

Bioinformatics. 28 (8): 1166–7. doi:10.1093/bioinformatics/bts091 (https://doi.org/10.1093%2
Fbioinformatics%2Fbts091). PMID 22368248 (https://pubmed.ncbi.nlm.nih.gov/22368248).
2. Fursov, M.; Novikova, O. (2008). "Multitasking software system for DNA analysis" (http://ww
w.bionet.nsc.ru/meeting/bgrs2008/BGRS2008_Proceedings.pdf) (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" (http://mosbiotechworld.ru/app/tez_09_03.pdf) (PDF).
Proceedings of the Fifth Moscow International Congress on Biotechnology. 3: 14–15.
ISBN 978-5-7237-0372-8.
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 978-5-7237-0372-8.
5. "NEW REBASE HOME" (http://rebase.neb.com/). rebase.neb.com. Retrieved 18 October
2019.
6. "Primer3 Input (version 0.4.0)" (http://bioinfo.ut.ee/primer3-0.4.0/). bioinfo.ut.ee. Retrieved
18 October 2019.
7. "Burrows-Wheeler Aligner" (http://bio-bwa.sourceforge.net/). bio-bwa.sourceforge.net.
Retrieved 18 October 2019.
8. "SAMtools" (http://samtools.sourceforge.net/). samtools.sourceforge.net. Retrieved
18 October 2019.
9. "TopHat" (http://ccb.jhu.edu/software/tophat). ccb.jhu.edu. Retrieved 18 October 2019.
10. "IU Webmaster redirect" (http://cufflinks.cbcb.umd.edu/). cufflinks.cbcb.umd.edu. Retrieved
18 October 2019.
11. "MACS - Model-based Analysis for ChIP-Seq" (http://liulab.dfci.harvard.edu/MACS/).
liulab.dfci.harvard.edu. Retrieved 18 October 2019.
12. "CEAS - Cis-regulatory Element Annotation System" (http://liulab.dfci.harvard.edu/CEAS/).
liulab.dfci.harvard.edu. Retrieved 18 October 2019.
13. "MrBayes | index" (http://nbisweden.github.io/MrBayes/). nbisweden.github.io. Retrieved
18 October 2019.
14. "ATGC: PhyML" (http://atgc.lirmm.fr/phyml/). atgc.lirmm.fr. Retrieved 18 October 2019.
15. CAP3 (http://seq.cs.iastate.edu/cap3.html)
16. "Macromolecular Structures Resource Group" (https://www.ncbi.nlm.nih.gov/Structure/MMD
B/mmdb.shtml). www.ncbi.nlm.nih.gov. Retrieved 18 October 2019.
17. "Spidey is superceded [sic] by Splign" (https://www.ncbi.nlm.nih.gov/spidey/).
www.ncbi.nlm.nih.gov. Retrieved 18 October 2019.
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 (https://doi.org/10.3233%2FISB-2012-0448).
PMID 22935964 (https://pubmed.ncbi.nlm.nih.gov/22935964).
19. "Illumina - iDEA Challenge" (https://archive.today/20130126033841/http://www.illumina.co
m/landing/idea/index.ilmn). Archived from the original (http://www.illumina.com/landing/idea/
index.ilmn) on 2013-01-26. Retrieved 18 October 2019.
20. "SAM" (http://samtools.sourceforge.net/SAM1.pdf) (PDF). Retrieved 18 October 2019.
21. Fursov, M. Y.; Varlamov, A. (2009). "UGENE - A practical approach for complex
computational analysis in molecular biology" (http://www.open-bio.org/w/images/c/c7/BOSC
2009_program_20090601.pdf) (PDF). Proceedings of the 10th Annual Bioinformatics Open
Source Conference: 7.

Official website (http://ugene.net)
Official website (http://unipro.ru/eng), UniPro
UGENE podcast (http://ugene.unipro.ru/podcast.html)
UGENE documentation (http://ugene.unipro.ru/documentation.html)
UGENE forum (http://ugene.unipro.ru/forum)
Лучший свободный проект России | Журнал Linux Format - все о Linux по-русски (http://
www.linuxformat.ru/foss-contest#foss2010-results)
(http://www.t-platforms.ru/ru/about/allnews/newsarchive/87--l-r-powerxcell-8i.html)permanent
dead link]
Retrieved from "https://en.wikipedia.org/w/index.php?title=UGENE&oldid=1064272350"
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22. "NIH: National Institute of Allergy and Infectious Diseases | Leading research to understand,
treat, and prevent infectious, immunologic, and allergic diseases" (https://www.niaid.nih.go
v/). www.niaid.nih.gov. Retrieved 18 October 2019.
23. "УНИПРО, Новосибирский центр информационных технологий. | СОФТ. Разработка,
тестирование, реинжиниринг, поддержка ПО" (http://unipro.ru/) ["UNIPRO, Novosibirsk
center of information technologies. | SOFT. Development, testing, reengineering, software
support"]. Retrieved 18 October 2019.
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