pLOT v1.0.4

   Version 1.0.4 represents quite a bit of under-the-hood modifications for speed and efficiency as well as the addition of quite a few new features.



Changes

1. Searching for amino acid sequences now allows you to opt for reading through stops.  When used with ambiguous AAs ("X") or gaps("-"), this lets you decide  whether to search for intact ORFs or those in which a stop codon may have been inserted.  This option is set in the "Find Sequence" window when the "Amino Acids" option is selected.

Example:
Without searching across stop codons, the search string "VSKGEELFT-QHDFXKSAMP-GMDELYK" to detect GFP-derivatives would detect the sequence

"VSKGEELFT.....................GMDELYK"

  but NOT the sequences
"VSKGEELFT-QHDF*KSAMP-GMDELYK"
or
"VSKGEELFT.....*.....QHDFFKSAMP-GMDELYK"

  This also gives you the option to search for ORFs of certain lengths by using a search string such as:

  "MNNNNNNNNNNNNNNNNN-*"  Where the number of Ns determines the minimum ORF length to find.

2. Enzymes now show how many times they cut at selection time in the enzyme selection window.

• This can be set in preferences to run automatically when opening short (Length < 15Kb), medium ( 15Kb > Length < 50Kb) or long ( Length > 100Kb) sequences. 

• The default is to detect only for short sequences automatically searching long sequences increases the load time for the file.

• Numbering can be run manually from the Restriction Enzyme selection window later if it hasn't been done automatically by clicking the "#" button in the Restriction Enzyme Selection window.

3. You can now get a list of cutters and non-cutting enzymes through the Tools-> Restriction Enzyme menu.  This will give you a list of all enzymes that cut and where in the sequence their sites are located or a list of all enzymes that do not have a site in your sequence.

4. Searching for restriction sites, primers and auto-annotation has been sped up significantly.  This is more obvious for larger sequences.

5. You now have the ability to zoom in on the plasmid from the View->Zoom menu (still a few minor changes needed in this though).

6. You can now toggle between linear and circular mapping from the Quick Menu at the top of the main window.

7. Pressing Ctrl + V allows you to specify a range of bp to view (Ex: "20 - 130" would show the sequence starting at bp 20 and through bp 130).

8. The Library Manager now allows you to view by category and rename/remove categories or delete categories and all items in it (right click on the item's category name to pop up this menu).

9. The "Find Sequences" window now allows you to select which found sites to add as tick marks.  A right click on the list lets you select all, de-select all, invert selection, and de/select all except currently selected item.

10. Minor corrections made to the restriction enzyme sequence file to correct a few incorrectly entered degenerate site sequences.  Added a bunch of Homing Endonucleases and the option to include or omit them from searches (in the restriction enzyme selection window.

Upcoming additions

• Fixes to the bugs below.
• Custom filtering of enzymes to show only those that cut within certain regions or certain numbers of times.

Known bugs
 - Overlap of labels in linear mode still occurs in very label-dense situations.
 - Linear arrows spanning the origin results in a floodfill glitch.

Download Links
*Due to certain file format changes, you MUST uninstall any previous version and running the complete v1.0.4 installation.  This will not make you lose custom library entries*
*Make sure all of the old files (especially the pLOT.dll) were deleted.  Windows occasionally does not remove them through the uninstall*

pLOT v1.0.4a Update
pLOT Sample Files
pLOT Manual v1.0 (Very rough draft)