UGENE

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'''UGENE''' is a free cross-platform [[bioinformatics]] software package.  
'''UGENE''' is a free cross-platform [[bioinformatics]] software package.  
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== Features ==
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{{Infobox Software
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[[UGENE]] has modular structure and almost all its functionality comes within plugins. Internally [[UGENE]] is designed with support of parallelism to make profit from using multicore computers.
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| name                  = UGENE
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| logo                  = [[Image:UGENE software package logo.svg|50px|UGENE logo]]
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| screenshot            = [[Image:UGENE-1.9.0-overview.png|250px|Working with genomic data in UGENE 1.9.0]]
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| developer              = Unipro
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| latest_release_version = 1.9.0
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| latest_release_date    = {{release date|2010|12|15|df=yes}}
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| programming language  = [[C++]], [[QtScript]]
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| operating system      = [[Cross-platform]]
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| language              = [[English language|English]], [[Russian language|Russian]], [[Czech language|Czech]]
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| genre                  = [[Bioinformatics]] toolkit
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| license                = [[GNU General Public License|GPL]]
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| website                = http://ugene.unipro.ru
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}}
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* Visual representation of annotated DNA or protein sequences
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'''UGENE''' is [[Free software|free]] [[Open source|open-source]] [[cross-platform]] [[bioinformatics]] software.  
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* [[Chromatogram | Chromatograms]] visualization
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* Integrated [[3D structure visualization | 3D viewer]] for files in PDB and MMDB formats
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* Integrated protein [[secondary structure]] [[prediction]] algorigthms based on GOR IV and PSIPRED
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* Integrated remote queries to NCBI, PDB, Swissprot, Uniprot databases
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* [[Multiple sequence alignment]] with port of [[MUSCLE]]
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* Easy-to-use search with [[Hidden Markov Models | HMM]] profiles using adopted [[HMMER|HMMER 2.32]] package
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* Integarion of the newest methods for [[Hidden Markov Models | HMM]] profile search based on [[HMMER | HMMER 3.0b2]]
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* Integration of primer3 package for [[Primer | PCR primers design]]
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* Search for transcription factor binding sites (TFBS) in DNA sequences
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* Restriction enzymes search and integration with [http://rebase.neb.com/rebase/rebase.html REBASE] restrictions enzymes database
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* Search for [[Repetitive DNA sequence | direct, inverted and tandem repeats]] in DNA sequences
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* Complete [[Smith-Waterman | Smith-Waterman algorithm]] implementation
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* Search for open reading frames
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* Designer for custom computational [[Workflow | workflows]]
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* A graphical interface for [[PHYLIP]] package
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== External links ==
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It integrates dozens of well-known [[Biology|biological]] tools and [[Algorithm|algorithms]], providing both [[GUI|graphical user]] and [[Command-line_interface|command line]] [[Interface|interfaces]]. Using [[#UGENE Workflow Designer|UGENE Workflow Designer]] one can arrange the required tools and [[Algorithm|algorithms]] into a [[Scientific_workflow_system|workflow]] schema.
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In order to provide maximum possible [[Computer_performance|performance]] '''UGENE''' utilizes multicore [[CPU|CPUs]] and [[GPU|GPUs]] to [[Program_optimization|optimize]] some of its [[Subroutine|computational routines]]. Another way to speed up [[Computing|computations]] is to use [[Amazon_EC2|Amazon EC2]] [[Cloud_computing|cloud]] resources.
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== Key features ==
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The software supports the following features:
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* Creating, editing  and annotating [[Nucleic acid sequence|nucleic acid]] and [[Protein|protein]] [[Sequence_(biology)|sequences]]
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* Search through [[Online_database|online databases]]:  [[National Center for Biotechnology Information|NCBI]], [[Protein Data Bank|PDB]], [[Swissprot|UniProtKB/Swiss-Prot]], [[TrEMBL|UniProtKB/TrEMBL]]
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* [[Multiple sequence alignment|Multiple sequence alignment]]:  [[Clustal|Clustal]], [[Multiple Sequence Comparison by Log-Expectation|MUSCLE]], [[List of sequence alignment software|Kalign]], [[MAFFT|MAFFT]], [[T-Coffee|T-Coffee]]
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* Online and local [[BLAST|BLAST]] search
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* [[Restriction enzyme|Restriction analysis]] with integrated [http://rebase.neb.com/rebase/rebase.html REBASE] [[List_of_restriction_enzyme_cutting_sites|restriction enzyme database]]
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* Integrated [http://frodo.wi.mit.edu/ Primer3] package for [[Primer (molecular biology)|PCR primers design]]
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* Search for [[Direct repeat|direct]], [[Inverted repeat|inverted]] and [[Tandem repeat|tandem]] [[Repeated sequence (DNA)|repeats]] in [[DNA]] sequences
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* Constructing [[Dot plot (bioinformatics)|dotplots]] for [[Nucleic acid sequence|nucleic acid sequences]]
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* Search for [[transcription factor]] [[binding site]]s ([[TFBS]]) with [[Position-specific scoring matrix|weight matrix]] and [http://wwwmgs.bionet.nsc.ru/cgi-bin/mgs/sitecon/sitecon.pl?stage=0 SITECON] algorithms
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* Aligning short reads with [http://bowtie-bio.sourceforge.net/index.shtml Bowtie] and UGENE genome aligner
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* Search for [[Open reading frames|ORFs]]
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* [[Cloning]] [[in silico]]
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* [[Protein structure|3D structure]] viewer for files in [[Protein Data Bank|PDB]] and [http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml MMDB] formats, [[Anaglyphs | anaglyph]] view support
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* [[Protein secondary structure]] prediction with [[GOR method|GOR IV]] and PSIPRED algorithms
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* [[HMMER|HMMER2]] and [[HMMER|HMMER3]] packages integration
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* Building (using integrated [[PHYLIP]] package) and viewing [[phylogenetic tree]]s
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* [[Sequence alignment|Local sequence alignment]] with optimized [[Smith-Waterman algorithm]]
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* Combining various algorithms into custom [[workflow]]s with [[#UGENE Workflow Designer|UGENE Workflow Designer]]
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* Search for a pattern of various algorithms’ results in a [[nucleic acid sequence]] with [[#UGENE Query Designer|UGENE Query Designer]]
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==User interface==
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<!-- [[Image:UGENE-1.9.0-alignment editor.png|thumb|right|250px|Alignment editor|250px]] -->
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The software has three main views to display [[Biological data|biological data]] on the user’s [[Display device|screen]].
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1. The '''Sequence view''' is used to visualize, analyze and modify [[Nucleic acid sequence|nucleic acid]] or [[Protein sequence|protein]] sequences. Depending on the sequence type and the options selected the followings views can be presented inside the '''Sequence view''' window:
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* [[Protein structure|3D structure]] view
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* Circular view
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* [[Chromatogram|Chromatogram]] view
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* [[Dot plot (bioinformatics)|Dotplot]] view
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2. The '''Alignment editor''' is used to visualize, analyze and modify a nucleic acid or protein [[multiple sequence alignment]].
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3. The '''Phylogenetic tree viewer'''.
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==UGENE Workflow Designer==
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<!-- [[Image:UGENE-1.9.0-wd.png|thumb|right|250px|Workflow Designer|250px]] -->
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'''UGENE Workflow Designer''' allows creating and running complex computational [[workflow]] schemas.
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The elements that a schema consists of correspond to the bulk of algorithms integrated into '''UGENE'''. Using the '''Workflow Designer''' one can also create custom workflow elements.
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The workflow schemas can be run both locally and remotely, either using the [[GUI|graphical interface]] or launched from the [[Command-line interface|command line]].
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==UGENE Query Designer==
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<!-- [[Image:UGENE-1.9.0-qd.png|thumb|right|250px|Query Designer|250px]] -->
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'''UGENE Query Designer''' allows a user to analyze a nucleotide sequence using different algorithms ([[Repeated sequence (DNA)|Repeats]] finder, [[Open reading frames|ORF]] finder, [[Position-specific scoring matrix|Weight matrix]] matching, etc.) at the same time imposing constraints on the positional relationship of the results obtained from the algorithms.
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A schema of the algorithms and constraints is either created from the [[GUI]] or edited as a [[plain text]].
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The results are saved as a set of [[Annotation#Computational biology|annotation]]s to a specified file in the [[GenBank]] format.
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==Supported biological data formats==
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* [[Sequence (biology)|Sequence]]s and [[Annotation#Computational biology|annotation]]s: [[FASTA format|FASTA]] (.fa), [[GenBank]] (.gb), [[EMBL]] (.emb), [[GFF]](.gff)
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* [[Multiple sequence alignment]]s: [[Clustal]] (.aln), MSF (.msf),  [[Stockholm format|Stockholm]] (.sto), [[Nexus file|Nexus]] (.nex)
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* [[Protein structure|3D structures]]: [[Protein Data Bank|PDB]] (.pdb), [http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml MMDB] (.prt)
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* [[Chromatogram|Chromatograms]]: ABIF (.abi), SCF (.scf)
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* Short reads: Sequence Alignment/Map(SAM) (.sam), [[ACE file format|ACE]] (.ace), FASTQ (.fastq)
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* [[Phylogenetic tree]]s: [[Newick format|Newick]] (.nwk)
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* Other formats: Bairoch ([[enzyme]]s info), HMM ([[HMMER]] profiles), PWM and PFM ([[Position-specific scoring matrix|position matrices]]), etc.
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==Release cycle==
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'''UGENE''' is primarily developed by [http://unipro.ru/ Unipro LLC]. Each [[Iteration#Project_management|iteration]] lasts about 6 weeks. By the end of [[Iteration#Project_management|iteration]] a [[Software release life cycle|release]] comes out. One can also download a development snapshot of the software.
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The features to be included into the next release are mostly initiated by users.
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==Awards==
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'''UGENE''' was awarded [http://www.linuxformat.ru/foss-contest#foss2010-results "The best FOSS project in Russia – 2010"] in the category "Group project" at the [[Linux Format]] magazine contest.
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==See also==
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* [[Sequence alignment software]]
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* [[Bioinformatics]], [[Computational biology]]
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* [[Free open source bioinformatics projects]]
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==Related software==
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*[http://www.csc.fi/english/research/sciences/bioscience/programs/ds Discovery Studio]
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*[[Gene Designer]]
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*[[Vector NTI]]
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*[[Geneious]]
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*[http://www.clcbio.com/main CLC Main Workbench]
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*[[MacVector]]
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*[http://www.crimsonbase.com/ QuickGene]
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*[http://www.biology.utah.edu/jorgensen/wayned/ape/ Ape]
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*[http://www.serialbasics.com/Serial_Cloner.html SerialCloner]
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==References==
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*{{cite journal | last=Fursov | first=M. | coauthors= Novikova, O. | year=2008 | title=Multitasking software system for DNA analysis |journal=Proceedings of the Sixth International Conference on Bioinformatics of Genome Regulation and Structure | volume=1 | pages=78 |url=http://www.bionet.nsc.ru/meeting/bgrs2008/BGRS2008_Proceedings.pdf | isbn=978-5-91291-005-0}}
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*{{cite journal | last=Fursov | first=M. Y.| coauthors= Oshchepkov, D. Y; Novikova, O. S. | year=2009 | title=UGENE: interactive computational schemes for genome analysis |journal=Proceedings of the Fifth Moscow International Congress on Biotechnology | volume=3 | pages=14–15 |url=http://mosbiotechworld.ru/app/tez_09_03.pdf | isbn=5-7237-0372-2}}
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*{{cite journal | last=Efremov | first=I. E.| coauthors= Fursov, M. Y; Danilova, Yu. E. | year=2009 | title=UGENE:  high performance genome analysis suite |journal=Proceedings of the Fifth Moscow International Congress on Biotechnology | volume=2 | pages=405–406 | isbn=5-7237-0372-2}}
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==External links==
* [http://ugene.unipro.ru/ UGENE homepage]
* [http://ugene.unipro.ru/ UGENE homepage]
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* [http://ugene.unipro.ru/podcast.html UGENE podcast]
* [http://ugene.unipro.ru/documentation.html UGENE documentation]
* [http://ugene.unipro.ru/documentation.html UGENE documentation]
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* [http://ugene.unipro.ru/forum UGENE forum]
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* http://www.linuxformat.ru/foss-contest#foss2010-results
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* [https://ugene.unipro.ru/tracker UGENE bug tracker]
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[[Category:Bioinformatics]]
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[[Category:Bioinformatics software]]
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[[Category:Free science software]]
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[[Category:Free software programmed in C++]]
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[[Category:Computational science]]
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[[Category:Software]]

Latest revision as of 15:39, 31 March 2011

UGENE is a free cross-platform bioinformatics software package.

UGENE
Working with genomic data in UGENE 1.9.0
Developer Unipro
Latest release 1.9.0 / 15 December 2010
Operating system N/A
Programming language N/A
Language English, Russian, Czech
Genre Bioinformatics toolkit
License GPL
Website http://ugene.unipro.ru

UGENE is free open-source cross-platform bioinformatics software.

It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces. Using UGENE Workflow Designer one can arrange the required tools and algorithms into a workflow schema.

In order to provide maximum possible performance UGENE utilizes multicore CPUs and GPUs to optimize some of its computational routines. Another way to speed up computations is to use Amazon EC2 cloud resources.


Contents

Key features

The software supports the following features:

User interface

The software has three main views to display biological data on the user’s screen.

1. 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 followings views can be presented inside the Sequence view window:

2. The Alignment editor is used to visualize, analyze and modify a nucleic acid or protein multiple sequence alignment.

3. The Phylogenetic tree viewer.

UGENE Workflow Designer

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

The elements that a schema consists of correspond to the bulk of algorithms integrated into UGENE. Using the Workflow Designer one can also create custom workflow elements.

The workflow schemas can be run both locally and remotely, either using the graphical interface or launched from the command line.

UGENE Query Designer

UGENE Query Designer allows a user to analyze a nucleotide sequence using different algorithms (Repeats finder, ORF finder, Weight matrix matching, etc.) at the same time imposing constraints on the positional relationship of the results obtained from the algorithms.

A schema of the algorithms and constraints is either created from the GUI or edited as a plain text.

The results are saved as a set of annotations to a specified file in the GenBank format.

Supported biological data formats

Release cycle

UGENE is primarily developed by Unipro LLC. Each iteration lasts about 6 weeks. By the end of iteration a release comes out. One can also download a development snapshot of the software.

The features to be included into the next release are mostly initiated by users.

Awards

UGENE was awarded "The best FOSS project in Russia – 2010" in the category "Group project" at the Linux Format magazine contest.

See also

Related software

References


External links

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