DNAやRNA、タンパク質のちょっとした解析に、GCGパッケージやCLIが苦手な上に市販のアプリケーションでは高すぎて手が出ない、フリーウェアの細切れでは面倒極まりないという方にお勧めするCLC Free Workbenchが4.0にアップデートしています。「CLC Free Workbench」CLC bio A/S
4.0にメジャー・バージョンアップということで、改めて特徴を示します (相変わらず英語そのままですけど…
)。Product features
- Bioinformatics features in Free Workbench
- Multiple alignment of DNA, RNA, and proteins
- Consensus sequence determination and management
- Conservation score along alignments
- Open reading frame determination
- Easy access to web-based protein and nucleotide search in GenBank, including download facilities and full graphical overview of sequence annotations of your choice
- Translation from DNA to proteins (all genetic translation tables)
- Reports with residue composition, molecular weight and iso electric point (for proteins)
- Neighbor-joining and UPGMA phylogenies
- Restriction site analysis and viewing
- Create reverse complement
- Shuffle sequence
- Option of viewing and graphical manipulation of bioinformatics analyses made in commercial workbenches from CLC bio
- Other features in Free workbench
- Full integration of data input, data management, calculations results, and data export. This eliminates time spent on manual data transfers between different programs and databases
- All types of files can be saved in local projects and launched from the program
- Detailed history log
- User-friendly graphical tools used in order to find and work with relevant regions of DNA, RNA and protein sequences
- Text-based sequence view
- Easy printing of reports and graphics
- Export of user-defined figures to various graphics file formats
- Import and export of data in a large number of file formats
- Option of working with different files and in different file projects at the same time
- Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
2007-07-19 16:07:12
4.0.1にバージョンアップしています。
# ていうか、立ち上げたらアラートが出た…
- Fixed error in conversion of old sequence data with lowercase characters
- Old data can now be converted through the help menu
- Fixed error when trying to save an element to non-selected location
- A few help updates
- Better license handling on Windows Vista
- Fixed error in alignment editing
2007-06-29 08:50:22
4.0にメジャー・バージョンアップしています。
- Highlights
- Full support for Windows Vista
- One-click switch between views (e.g. circular and linear sequences views)
- New annotation table - easy overview and filtering of annotations
- State-of-the-art layout of annotations
- Better and more intuitive handling of files (you can now access the files directly on the file system)
- It is now possible to "Save as"
- Easily expand selections using the mouse
- Improvements of restriction site analysis
- All the details
- General use
- One-click switch between views (e.g. circular and linear sequences views). There is a new row of buttons at the bottom of each view which you can click to switch the view. Pressing Ctrl (Command on Mac) while clicking creates a split view of the two.
- Pressing Ctrl (Command on Mac) while rolling the scroll wheel of the mouse can now be used to zoom in and out (only possible for mice with scroll wheels).
- Many right-click menu items have now icons to make it easier to navigate the menus.
- Simplifying the task of creating a new sequence. Rarely-used elements like "Keywords" and "Comments" have been removed from the dialog, and the two steps have been merged into one.
- You can now use I (inosine) in nucleotide sequences.
- Better choices for the resolution of exported graphics.
- Sequence views
- Easily expand selections using the mouse. When you have made a selection, place the mouse cursor on the edge of the selection, and you can now adjust the selection. This is also possible for each part of a multiselection.
- Quick-jump to annotations. In the Side Panel under "Annotation types", it is now possible to click a quick-jump button which lets you go directly to the annotation. This provides a very quick and easy way of browsing annotations.
- The names of annotations are now repeated on each new line in a wrapped sequence view.
- The user can now specify which symbol to use in an alignment consensus sequence in case of ambiguities.
- In nucleotide sequence views, you can introduce a space for every three characters to visualize codons. In the Side Panel under "Sequence layout" there are now several options for "Spacing": Every 10 residues, every 3 residues in three reading frames.
- It is possible to search in text views. In the Side Panel, there now is a "Find" group where you can enter a text to search for.
- You can now hide labels in sequence views. This is particularly convenient with long sequence names taking up a lot of space.
- Import and export
- Pasting simple sequence text (like ATCGTACGTA) in the Navigation Area automatically creates a new sequence.
- Import and export of view settings (the settings saved in the Side Panel). In the Preferences dialog (available from the Edit menu), in the "View preferences" you can now export and import the View settings.
- All tables can be exported in a CSV format (semicolon-separated). When exporting sequences in this format, the annotations are exported.
- Restriction site analysis
- "Restriction Sites Analysis" has been renamed to "Create Restriction Map" and the dialogs are more intuitive to use.
- It is now possible to filter the list of enzymes to easily pick a specific enzyme.
- It is easier to set the number of cut sites for the restriction enzymes to be displayed
- When you open an enzyme list, you can select a number of enzymes, right-click and "Create New Enzyme List from Selection". This makes it easy to create subsets of enzyme lists. Combined with the table's filter, this makes it easy to extract e.g. restriction enzymes from a specific vendor.
- Data handling
- Copy an element in the Navigation Area by dragging while pressing the Ctrl button (Command button on Mac)
- Filter elements in the Navigation Area (to show e.g. only nucleotide sequences). The filter is available from the small tool bar above the Navigation Area.
- When selecting elements for analysis, only the relevant elements are shown (e.g. only nucleotide sequences are visible when selecting sequences for Restriction Site Analysis).
- When selecting elements for analyzes (in the select elements dialog), you can right-click a folder and add all the elements in that folder.
- Possible to sort elements alphabetically
- One-click renaming of elements. Simply click an element which is already selected, and you can type a new name directly.
- Recycle bin is now visible and you can easily restore deleted elements simply by dragging to the desired folder.
- In the File menu, there is a "Save As" menu item. It saves the opened element under a new name.
- Easily collapse all folders in the Navigation Area by clicking the "Collapse All" icon in the small tool bar above the Navigation Area.
- Plug-ins and licenses
- Plug-ins are now installed for all users of a computer.
- Licenses also apply to all users of the computer.
- General use
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ではなく、エレメント・ギャラリーなるさらに怪しげなUI
。考えてみれば、ATOK2006にアップグレードした辺りから妙に頭が悪くなったような気がします。文節の切り方然り、変換の仕方然り…。具体的な例は、その都度怒り心頭に発していたので、ストレスを溜めないために忘却の彼方へ捨て去りました
。
2006-10-25 08:55:51
。
。とりあえず、復帰プログラムくらいさっさとリリースしろよといいたいところですが、あくまでもアップデートで提供するつもりみたい…。ユーザーをなんだと思っているのやら…
。