CloneManager

What works

• Files: (finally works)
• Saving cm5 files
• Loading cm5 files
• Export
• Send to file
• Sequence only
• Commented GenBank
• Import from clipboard
• View
• Map
• Restriction Map
• Sequence
• Features
• Info
• Zoom
• Send view to file
• htm
• rtf
• txt
• Sequences
• Edit sequence manually
• Discover
• Open reading frames
• Operations
• Process Molecule
• Invert molecule
• circularize molecule
• Primer values profile
• Clone
• Find enzyme sites
• find single cutters works
• Cut with
• Enzyme
• Base Position
• Ligate
• Ambiguous orientation is detected
• Modify ends
• Custom
• Klenow fill-in
• 3'-5' exo
• Auto Scan
• Primer
• Primer List
• Add primer
• Analyze
• One primer analysis
• Primer pair analysis
• All primer tests seem to work
• Find primers that bind
• finds correct primers and displays them in sequence and map
• Create product
• Visualizations
• Map
• Displays linear and circular DNA
• Displays ORFs
• Displays enzyme sites
• Displays primers
• Enhanced View
• Copy hi-Res Bitmap to Clipboard
• Export to BMP
• Export to PNG
• Change text font size and style
• Change feature style and color
• Enzyme sites
• wipe all
• Primer sites
• wipe all
• Sequence visualization
• Displays enzyme sites (beware, not sure if this works 100%)
• Displays primer sites
• Displays modified ends after enzyme treatment
• Features panel
• displays ORFs
• displays regions
• displays labels
• Discover
• Blast Internet search: surprisingly this also worked. Working sequence was transmitted and BLAST report was accessible through internal browser. Works, but reaction was sluggish.
• Window
• Cascade
• Tile horizontally
• Tile vertically
• Arrange icons

What does not

• Visualizations
• Export to JPG
• Export to TIFF
• --> image distorted when opened in GIMP 2.
• Operations
• Compare to sequences
• Assembled: strange character at +1
• Editing (Pencil symbol) led to the error: "An invalid argument was encountered"
• View
• Send view to clipboard

Workarounds

What was not tested

All the rest of the features.

Hardware tested

Graphics:

• GPU:
• Driver:

Additional Comments

CloneManager finally runs almost flawlessly on Linux :) Ubunutu 12.04.4 LTS precise IN VIRTUAL BOX Native wine package from Ubuntu 12.04 is too old (as of 2014/04/12) and does not work with CloneManager. Instead I installed Winehq from third party binaries from https://launchpad.net/~ubuntu-wine/+archive/ppa/+sourcepub/3740586/+listing-archive-extra No extra configuration neccessary!