UGENE

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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.
[[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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* View and analysis of annotated [[DNA]] or [[protein]] sequences
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* Visual representation of annotated DNA or protein sequences
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* Huge files support, native support of [[gzip | gzipped]] documents
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* [[Chromatogram | Chromatograms]] visualization
* [[Chromatogram | Chromatograms]] visualization
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* Search for [[Open reading frames | ORFs]]
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* Integrated [[3D structure visualization | 3D viewer]] for files in PDB and MMDB formats
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* Integrated support of search requests to [[National Center for Biotechnology Information|NCBI]] databases
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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
* [[Multiple sequence alignment]] with port of [[MUSCLE]]
* [[Multiple sequence alignment]] with port of [[MUSCLE]]
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* Easy-to-use search with [[Hidden Markov model | HMM]] profiles using adopted [[HMMER]] package
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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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* Integrated 3D viewer for files in PDB format
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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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* Designer for custom computational workflows
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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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* 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 and inverted repeats]] in DNA sequences
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* Complete [[Smith-Waterman | Smith-Waterman algorithm]] implementation
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* Search for ppen reading frames
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* Designer for custom computational [[Workflow | workflows]]
== External links ==
== External links ==

Revision as of 09:01, 10 July 2009

UGENE
File:UGENE 1 2 0 screenshot.png
UGENE viewing Escherichia coli complete genome
Developer Unipro
Latest release 1.2.0 / September 19, 2008
Operating system N/A
Programming language N/A
Language English, Russian
Genre Bioinformatics toolkit
License GPL
Website http://ugene.unipro.ru

UGENE is a free cross-platform bioinformatics software package.

Features

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.

External links

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