Unipro UGENE 1.4.2

Unipro UGENE 1.4.2 is an open-source bioinformatics project which aims to integrate most of the important molecular biology tools within a single graphical environment. UGENE runs on Linux, Windows and MacOS platforms and is able to utilize resources of modern multi-core and GPU hardware.

Major Features:

1. User Interface:
   
   • Visual and interactive process of analysis
   • Workflow Designer to create computational workflows
   • High-quality, publication ready visualization
   • Native look-and-feel on Windows, Linux, Solaris, MacOS
2. Design and extensibilty:
   
   • A script language to create new tasks and GUI elements
   • Support for pluggable modules
   • Active computational tasks do not block user interface
3. Hardware scalability:
   
   • Supports most of modern hardware: all modern 32/64-bit Intel and AMD processors,
   • IBM Cell and Sun Sparc processors
   • Customizable algorithms library: multicore computers, GPU blocks, high performance clusters
4. Availability and cooperation:
   
   • Free and open source
   • Can be used for education in schools and universities
5. Visual representation of annotated DNA or protein sequences
6. Huge files support, native support of gzipped documents
7. Chromatograms visualization
8. Search for ORFs
9. Integrated support of search requests to NCBI databases
10.  Multiple sequence alignment with port of MUSCLE
11.  Easy-to-use search with HMM profiles using adopted HMMER package
12.  Integrated 3D viewer for files in PDB and MMDB formats
13. Designer for custom computational workflows
14. Search for transcription factor binding sites (TFBS) in DNA sequences
15. Restriction enzymes search and integration with REBASE restrictions enzymes database
16. Search for direct and inverted repeats in DNA sequences
17. Complete Smith-Waterman algorithm implementation

Enhancements:

• Introduced Undo/Redo support for MSA Editor
• Search in MSA Editor now works more accurate with different case of pattern
• Extra filters for SITECON search procedure added
• Now UGENE is capable of reading CLUSTAL X files
• Smith-Waterman plugin became more accurate
• Some concurrent-related bugs in MUSCLE fixed
• Some Qt 4.5 compatibility issues fixed
• Lots of minor stability fixes