Unipro UGENE 1.35

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.

Main features:

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.