Bug#623731: RFP: ugene -- integrated bioinformatics tools
Package: wnpp
Severity: wishlist
* Package name : ugene
* URL : http://ugene.unipro.ru/
* License : GPL
Description : integrated bioinformatics tools
Unipro UGENE: Integrated Bioinformatics Tools
UGENE is a free cross-platform genome analysis suite.
It works perfectly on Windows, Mac OS or Linux and requires only a few clicks to install.
Features
Screenshots
Feature-rich sequence viewer and annotator
Swine flu in UGENE
Workflow Designer visual interface
Workflow Designer
Multiple sequence alignment editor
Multiple alignment
Integrated tools
Multiple sequence alignment using MUSCLE 3, KAlign, Clustal;
HMM profiles build and search, based on the source of HMMER 2 and HMMER 3;
PCR Primers design using Primer 3;
Cloning in silico capabilities;
Queries to NCBI BLAST and CDD databases;
Protein secondary structure prediction using GOR IV and PSIPRED;
Phylogenetic analysis with Phylip;
Search for restriction enzymes and integration with REBASE;
Extremely fast repeat finder;
DNA reference assembly using Bowtie;
Search for transcription factor binding sites using SITECON;
Protein back translation;
ORF finder;
Complete Smith-Waterman algorithm implementation;
Support for external tools: BLAST+, MAFFT, T-Coffee.
User interface
Visual and interactive genome browsing including circular plasmid view;
Multiple alignment editor;
Chromatograms visualization;
3D viewer for files in PDB and MMDB formats with anaglyph stereo mode support;
Phylogenetic tree viewer;
Dot plot visualization;
Query designer enables search for complex annotation patterns;
Easy to use workflow designer for custom computational workflows.
High performance computing in UGENE
Complete support of modern multicore processors and SSE instructions;
Out of the box support of modern GPUs using NVIDIA CUDA and ATI Stream;
Support for cloud computing: running computational tasks on Amazon EC2 cloud;
Support for supercomputers and distributed computing.
Cooperation
Can be used for education purposes in schools and universities;
Features to be included into the next release are initiated by users;
UGENE team is ready for collaboration in related projects, both free or commercial.
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