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Unipro UGENE v1.6.0 changes:
New plugins:
New features and bug fixes:
- Search for tandem repeats added introduced in Repeat Finder plugin;
- Project files transferability support;
- "Export project" feature;
- Remote databases interaction: NCBI, PDB, Swiss Prot;
- BioStruct3D plugin: anaglyph stereo mode;
- Sequence editor: several minor improvements and bugfixes;
- Lots of minor stability and usability fixes.
Unipro UGENE v1.5.2 changes:
New plugins:
- MUSCLE 4 - a port of the newest tool for multiple sequence alignment by Robert C. Edgar;
- CUDA Support - an utility plugin which makes possible using NVIDIA graphical processing units for accelerating computational algorithms (Windows only).
New features and bug fixes:
- CUDA-accelerated Smith-Waterman algorithm is ready to use for Windows users;
- The one of the most awaited features: sequence editing has been added;
- Primer 3 integration has been finished - a complete set of preferences is available now;
- Exporting annotation tables to CSV has been provided;
- New workers have been added to Workflow Designer: Sequence splitter and Remote request;
- Collecting statistical reports feature has been added. See the dialog on the first launch of v1.5.2;
- HMM2 models support has been added to HMM3;
- Filtering by hits number has been added to enzymes search;
- Now UGENE drops 'fantom' documents on project closing;
- Bug with incorrect handling of sequence range selectors has been fixed in SSP dialog;
- SSP algorithms, Primer3 and PDB parser now work correctly when launched in parallel;
- A serious bug affecting Fedora users has been fixed in PSIPRED.
Unipro UGENE v1.5.1 changes:
New plugins:
- BALL - adds new types of molecular surfaces to UGENE 3D viewer
New features and bug fixes:
- New feature: sequence line view and MSA editor now support saving fancy screenshots
- Congene crash on windows has been fixed
- HMM3 crash with malformed models has been fixed
- Crash with simultaneous primer3 tasks has been fixed
- Remote request is now stable when launched on Linux systems
- Missing Smith-Waterman search is restored
- Primer3 tasks now support cancelling
- Choosing selection color has been added to 3D viewer
- Sequence selection in Detailed View has been fixed a bit
Unipro UGENE v1.5.0 changes:
New plugins:
- HMM3 - modern set of tools for HMM profiles build and search, based on HMMER 3.0b2
- Primer3 - integration of the primer3 tool for PCR primers design
- GOR IV and PSIPRED - protein secondary structure prediction tools
- congene - command-line version of UGENE which allows user to launch workflows from the command-line
New features and bug fixes:
- BioStruct3D viewer: molecular surface visualization
- Loading remote documents from PDB, Uniprot, Swissprot
- 'Create document from text' feature
- Annotations editing significantly improved
- Some critical bugs in Qt 4.5.0 are workarounded
- Stability fixes for parallel MUSCLE: deadlock prevention
Unipro UGENE v1.4.2 changes:
Improvements and bugfixes:
- 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
Unipro UGENE v1.4.1 changes:
Improvements and bugfixes:
- Color schemes support in Alignment editor
- A camera lock option for multiple 3D protein models
- Sequence viewer optimized to be used with large amount of annotations (up to 1 million)
- Sequence viewer can show qualifier values instead of annotation names now
- Chromatogram viewer: quality values are now shown by default for ABIF files
- Several stability and compatibility issues fixed in BLAST, MUSCLE and HMMER modules
- A number of minor stability fixes
Unipro UGENE v1.4.0 changes:
New features:
- New plugin: Smith-Waterman. A complete implementation of Smith-Waterman algorithm
- New plugin: Restriction Enzymes. Marks restriction enzymes in a sequence. Supports 'bairoch' file format provided by REBASE database
- New plugin: Repeats Finder. Searches direct and invert repeats in DNA sequences. Optimized for huge sequences
- New plugin: DNA Statistics. Exportable statistical reports
- Workflow Designer: runtime state visualization of executed schema
- Workflow Designer: integrated support of workflow samples
- Workflow Designer: resizable items + snap to grid, customizable colors and fonts.
- MSA Editor: show non-gapped offsets for each sequence in alignment
- MSA Editor: a tool to search patterns in alignment
- Sequence view: support scale locks and synchronization for different sequences
- Sequence view: support for arbitrary number of rulers created by user
- BioStruct3D viewer: export of 3D PDB and MMDB models into 2D vector format (SVG)
- BioStruct3D viewer: a fast and extensible way to link active 3D model to Web resources
- Project view: supports 3 different view mode: grouping data objects by type, by document and flat view
- Project view: list of data objects for unloaded documents is shown
- Performance: UGENE now allows to specify ideal count of CPUs, threads and memory to be used
- DNA Export plugin: export of arbitrary multiple sequence alignments to FASTA format
- New file formats supported: FASTQ, MMDB (plain text ASN)
- Support for large (> 10Gb) files indexing for a fast data access
- Custom application GUI themes supported. Windows version of UGENE uses Office GUI theme by default.
Improvements & bugfixes:
- MUSCLE plugin: part of the original algorithm was optimized to utilize multicore CPUs.
- HMMER plugin: SSE2 implementation of the algorithm was added;
- HMMER plugin: hmmsearch now works in parallel mode for a single sequence by default (gives >30x boost for quad-core CPU when used with SSE2)
- SITECON plugin: >50 new prokaryotic profiles to recognize transcription factor binding sites added
- Most the views and dialogs got performance and usability improvements
- Workflow Designer: now preserves additional info of processed data (like accessions, source etc) throughout overall computation.
- Workflow Designer: write tasks now provide controls to override existing target file (either overwrite, append or rename).
- Project view: supports relocation and copying of documents.
- Annotation creation: new annotations now can be added to an unloaded annotation table object. The object is automatically loaded in this case.
- MSA Editor: allows to change fonts, initial and limited support for zooming operations
- BioStruct3D viewer: support for single structure with multiple 3d models
Unipro UGENE v1.3.3 changes:
Improvements and bugfixes:
- A QT4.4 bug that prevents correct rendering of OpenGL widgets on some Linux platforms is work-arounded.
- Group naming erorrs when nested groups used is fixed.
- A new and more complete implementations for ABIF and SCF formats added.
- Fixed bug that prevented 'z' char to be used in annotation names.
- Annotations tree widget performance improved.
- Sitecon plugin now processes custom regions correctly.
- Workflow Designer crash when multiple iterations are used is fixed
- For very short DNA sequences without 'U' and 'T' letters DNA genetic code is used now by default instead of RNA.
- 'Tab' characters in FASTA and Genbank plain text formats do not produce error messages anymore.
- Ubuntu package of UGENE was split into 2 packages (data and gui) to satisfy Ubuntu packaging rules.
Unipro UGENE v1.3.2 changes:
Improvements and bugfixes:
- Fixed issue that can disallow to open more that 1 view on some 64-bit systems.
- Fixed crashes when several PDB models are opened side by side in a single 3D-viewer window.
- Fixed crash when opening ABI file with a very short sample name.
- Added "Check For Updates" menu.
- Fixed crash in "Find pattern" dialog when complement strand is selected for amino sequences.
- Fixed chromatogram objects association for ABIF and SCF files.
- Fixed genetic code autodetection for PDB file format.
- Improved docked labels appearance for Linux and Mac OS X platforms.
- Improved 'Add object to view' menu logic.
Unipro UGENE v1.3 list of changes:
New features:
- Linux support. Packages for Fedora and Ubuntu
- New plugin! Workflow Designer: allows to design custom computational workflows
- New plugin! SITECON: search for Transcription Factor Binding Sites (TFBS) in DNA sequences
- New plugin! BioStruct3D: 3D molecular protein and DNA structure viewer for PDB format
- Stockholm and PDB formats support
- Browsing multiple sequences side by side in a single sequence view window
- Sorting by annotation qualifier values
- 'db_xref' qualifiers made interactive and are linked to corresponding web databases
- Translation and complement strands can be hidden in sequence view
- Support for localization. English and Russian translations are included into the default distribution
- Tasks can generate detailed reports now
Improvements & bugfixes:
- Task progress is now shown in status bar
- Critical fix: Memory leaks and crashes fixed in code that integrates MUSCLE package into UGENE
- Critical fix: Default parameters of HMMER-related dialogs are now the same as in original HMMER
- Logs view now do not show traces by default
- Drag&drop support for all file types supported by UGENE
- >100 other minor fixes, usablity and performance improvements !
Unipro UGENE v1.2 list of changes:
New features:
- MacOS v10.4 and v10.5 support.
- Multiple sequence alignment editor. MUSCLE alignment algorithm integrated as a separate plugin.
- New plugin! ORF Marker: Searches for ORFs in DNA-sequences.
- New plugin! ChromaView: The plugin integrates chromatogram viewer into 'Annotated DNA View'
- New plugin! Remote request: Annotates selected DNA-sequence regions by sending requests to BLASTn, BLASTp and CDD servers. Can be extended to use other servers with scripts.
- New plugin! UMUSCLE: Adds MUSCLE alignment algorithm to the system.
- Files located on remote servers can be added to project by HTTP protocol
- Scripting support for custom WEB-based BLAST/CDD-like queries. Binding for all GUI/Utility classes and ability to create any algorithms using script.
- DNAGraphPack plugin supports 4 new graph types: GC & AT deviations, Karlin Signature Difference and Informational Entropy
- All genetic translation tables of Genbank database are supported and can be selected by user.
- SCF format support added.
- Support for unloading documents without removal them from a project.
Improvements & bugfixes:
- UGENE can be associated to open all file types it supports from command line. File binding comes by default with Windows installer.
- Better integration of uHMMER plugin with Annotated DNA View and MSA Editor
- DNAGraphPack plugin now shows interval based graphs for large zooms to keep min/max information precise.
- Drag&Drop functionality between 'Project View' and 'Annotated DNA View'
- Dozens of GUI, performace and compatibility improvements and bug fixes.
Unipro UGENE v1.1 list of changes:
New features:
- EMBL, ABI, CLUSTALW and raw sequence file formats supported.
- Custom document format settings option added when adding documents to project.
Use this option if you need to merge all DNA sequences found in document into a single sequence.
- New plugin: uHMMER . This is a port for hmmbuild, hmmcalibrate and hmmsearch tools from HMMER2.3.2 package
- New plugin: DNA Export. This plugin adds functionality to export various types of DNA sequence selection to FASTA file format.
- Starting from this version UGENE works transparently with compressed documents in GZIP format.
For example, compressed files can be added to project.
- New plugin: DNA Annotator. This plugin adds annotation based searches to runtime.
Current version allows to find regions that contain a predefined set of annotations.
Improvements & bugfixes:
- Multi-selection support added for annotations tree used in 'Annotated DNA View'.
- Annotations' colors, placement and visibility properties were made customizable.
- "Find DNA sequence" algorithm was tuned. Several bugs fixed.
- A lot of minor GUI and performance improvements.
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