What's new in AmplifX 1.7.0
Nov 22, 2013
- The Mac version is now a Cocoa application (compatible Mac OS 10.9 Mavericks and Retina displays)
- Very big sequences support (> 1 million nucleotides)
- Huge improvement in speed for almost all time consuming operations : sequence and primer list loading, match searches, primer design, ...
- The program is now distributed as a multilingual bundle (still only in english and french but translators are welcome)
- Multi-criteria sorting of primer list (see the new menu "primers > Sort using multiple criteria...")
- Ability to change the primer order in the list by drag and drop
- New interface element (slider) in the main window that allow to quickly change the required number of perfect matching 3’end nucleotides in the match search algorithm (without going to the Preference window)
- The menu "paste complement strand" now works into the field "use this primer" in the primer design window.
- Behavior improvement of the menu "Undo"
- Graphic view zooming improvement
- And a lot of bug fixes and algorithm corrections
New in AmplifX 1.7.0 Beta 2 (Sep 30, 2013)
- Previous beta (1) bug fix : changes in the comment field are take into account as expected.
- Previous beta (1) bug fix : U/u are converted into T/t as expected and not deleted !
- Improvement of the primer list saving process when the destination volume has been disconnected (automatic network reconnection or standard dialog to choose an other destination volume)
New in AmplifX 1.7.0 Beta 1 (Sep 30, 2013)
- The Mac version is now a Cocoa application !
- Very big sequences support (>1M nucl.)
- Huge improvment in speed for almost all time consuming operations : sequence and primer list loading, match searches, primer design, ...
- The program is now distributed as a multilingual bundle (still only in english and french but translators are welcome)
- Multi-criteria sorting of primer list (see the new menu "primers > Sort using multiple criteria...")
- Ability to change the primer order in the list by drag and drop
- New interface element (slider) in the main window that allow to quickly change the required number of perfect matching 3’end nucleotides in the match search alogorithm (without going to the Preference window)
- Bug correction : no more -1 offest when redefining origin at the insertion point.
- Bug correction in the Linux version : crash of the program sometimes after a default primer list was defined
- Bug correction (all versions) : crash after clicking an amplicon and load a new primer list
- The menu "paste complement strand" now works into the field "use this primer" in the primer design window.
- Behavior improvment of the menu "Undo"
- No more lost of comments that could happen in certain circumstances
- The user can choose to keep informations ("infos" tab) of each clicked graphic element of the PCR map or to keep only the last one (as previously)
New in AmplifX 1.6.2 (Feb 7, 2013)
- IMPORTANT : fix a serious bug in version 1.6.1 that can corrupt primer list IF AND ONLY IF one saves primer list AFTER sorting it and add new primers since yet. IF it’s the case, please contact me with the feedback form so I can help you to repair your primer list !
- Improve : after reseting the preferences, the default column widths are restored
- Improve automatic ID proposal for new primers
New in AmplifX 1.6.1 (Jan 12, 2013)
- Fix: no more crash when opening primer lists saved by AmplifX prior to 1.5.0
- Improve: Alert box
New in AmplifX 1.6.0 (Jan 10, 2013)
- New features:
- Linux version (32bits - GNOME). Tested on Fedora 17 and Ubuntu 12.04 with GNOME-classic (not compatible with Unity!).
- Filtering system of the primer list: as you type on the classic search field, the primer list is filtered instantaneously! Possibility is given to restrict to the matching primers.
- New column in the primer list: a color code that is associated to category or family (or anything one needs). The colors are used in the graphic map to figure out the corresponding matches. -*Possibility to limit the size of the amplicons (default=3000 bp) (see the text field near the "run PCR" button.
- Primers can match even if they exceed the target sequence (limit is 254 nucl.)
- New menu: "invert case". Specially useful with the new primer design options (see above)
- Windows version is distributed with a Setup (thanks to Inno Setup)
- Mac version is distributed on a disk image (.dmg)
- New menu: "Window"
- New menu "New primer list"
- A click in a “match” automatically selects the primer on the list. But the active tab remain the same (previously it systematically showed the info’s panel)
- Primer design: add the criteria "GC clamp" to design primers ending with a chosen number of (G,C).
- rimer design: new search option for primers ending with N nucl matching on part of the target sequence typed as lowercase. It can be of special interest to design specific primers on a mutant for example.
- Primer design: the special options are hidden to not overload the interface
- Primer design: No more upper size limit for the amplicon size
- The match information (info tab) displays the start and end position on the target.
- Primer list: if the ID is found in duplicate, an alert (duplicate ID) is added after it.
- Application launching: if the program try to mount a network volume: a window tells the user to be patient. The timeout is managed by the operating system and not by AmplifX.
- Graphic map: as the mouse is over a match, the corresponding amplicons are automatically sorted on the top of the map.
- Application launching: if a new version is available a message is shown.
- - Primer list: one can now choose which columns one want to export and the order.
- Degenerated primers: a new option (in the preferences window) tell the program to not try to match primers too much degenerated (default: 256) (the degenerated sequence ACGTSN means A, C, G, T, (C or G), (A or C or G or T) and the fold of degeneracy is 1x1x1x1x2x4=8
- One can add multple pairs of primer from the design Window to the primer list
- A new dialog while importing primers allows the user to tell which columns and which order they are in the source file.
- [Mac] Target sequences can now be open by drag and drop onto the dock icon.
- Drag-n-drop anywhere on the main window allows to open primer list and target sequences
- A splitter separate the window in height to customise the respective height of the upper elements (primer list and all the stuf in the tab viewer) and the graphic map above. (It prefigures some new features coming soon!)
- Improvements:
- "Run PCR" button behavior enabling/disabling improved.
- Primer list contextual menu improved
- Graphic map zoom improved
- Menu "paste complementary strand"
- The locking system used to avoid overwritten by an other user uses an invisible file which a name beginning with a ’.’. These names are not allowed on every system so AmplifX uses now an alternative name with ’__’ at the beginning.
- Primer list edition improved (very annoying bugs in Windows are now corrected) Search function improved, the "search on lower strand" functions.
- Mac OS: Command H is used as waited for hide AmplifX and not to show the help.
- Mac OS: Dramatic improvement in trimming a pasted sequence.
- Primer design: the "search" button is disabled after a search until the criteria or the sequence are changed (to avoid clicking by mistake and wait again!)
- No more alert message with big target sequence (the program can manage very big sequences depending on the performance of your PC/Mac)
- Primer design: coherence between each search criteria is improved
- Corrections and coherence in the numbering of the size and base position of matches (always the 5’ of the primer and not the 5’ of the match in the target sequence)
- Primer design: Correction of the difference of one in the criteria fields and the return values of the found primers.
- Bug correction of the deletion of one nucleotide after "redefining the origin"
- Windows: zoom animation improved.
- Improve: primer list editing
- Improve: behavior with big target sequences
- Improve: speed in primer list loading
New in AmplifX 1.5.4 (Oct 28, 2008)
- Minor correction of version 1.5.3: calculation of amplicon size was distorded by previous correction of reverse primer position (thanks one more time to Savio Chan, current champion in bug detection!)
New in AmplifX 1.5.3 (Oct 21, 2008)
- Cosmetic: suppression of text overlapping in some alert dialogs
- New option “exclude lowercases” in the primer design’s window (yet implemented in version 1.5.2 but not explained!). This option allows for example to find primers that don’t match against lowercase typed nucleotides in the target sequence. It’s especially useful, for example, to make specific primers for one sequence in a family (type non conserved bases in uppercases) or in the contrary for primers matching conserved regions (type conserved nucleotides in uppercases).
- Redefining the target sequence origin can now be done by a right-click onto the target sequence after inserting the cursor at the desired position.
- Primer design: correction of the calculation of the reverse primer position in the result’s list (bug reported by C. Savio Chan)
- Primer design: adding information to the primers when added to the current primer list: target name, matching position, design date, …) (Feature asked by C. Savio Chan.)
- Preference window: correction of min and max cutoff scores for weak and strong matches. Sorry this bug appeared in the previous version because of an anticipation of a next major rewriting of the virtual PCR algorithm. (Thanks one more time to C. Savio Chan to saw it.)
- Search function: correction of some bugs in the “search all occurrences” option.
New in AmplifX 1.5.2 (Sep 16, 2008)
- Normal behavior of esc key when the cursor is in a cell of the primer list: the cell simply looses the focus and no spaces are typed. (Thanks to Lars Henning to have reported this bug.)
- Correction of the GeneBank importation: a G was systematically added at the beginning.
- Possibility to directly import ApE file formats (GenBank format in fact with special file name extension.)
- Correction of a crashing bug when importing target sequences with some special Unicode characters (thanks to Damien Hermand to report this bug.)
- Keeping registration key when restoring pref files with default values. (Sorry for guys that needed to register AmplifX again!)
New in AmplifX 1.5.0 (Jul 10, 2008)
- Modification of primer list format (automatically updated when open with AmplifX 1.5.0 or superior).
- To work on a shared primer collection into a team or a lab, the best way is to use the same primer list file into the local network. To help working in this way, now, AmplifX manages a locking system that allow only the first user to write into the primer list and save changes. The other users can only read the file and must � save as... � if they make some changes. After the first user close the file, the lock is destroyed and one other user can reload the modified primer list and make its own changes.
- A new column � Owner � is especially useful in the context of shared primer list. Its entry is made easier by a scrolling menu.
- Heights and widths of the columns of the primer list and size and position of the main window are restored at each launching of AmplifX.
- To each new added primer, an id is automatically created (it can be changed by hand, of course). The program analyses previous ids and increment them: they can be constructed with any prefix and a number possibly formatted with a constant number of digits: example Pr0001, Pr0002,...
- End of line characters are forbidden into any primer list fields: Enter and Return keys are managed in the same way as the tab key: editing of the next field.
- Add amplicon size information into found primer pairs of the Primer design window.
- The primer design window is not resizable anymore.
- Management of expiration date for the beta releases of AmplifX -Drag and drop is now properly managed into the target sequence text field: dragging from an outside source (text editor, web page) insert recognized ATGC (upper and lower cases) at the insertion point. But dragging from the target sequence field itself is forbidden. Because it has appeared to be triggered accidentally (while playing with selection for example).
- Automatic fetch for AmplifX updates.
- Automatic request for registration (after using AmplifX for a while) by an integrated form. (Note: registering and giving some feedback is not very time consuming but very motivating and interesting for the kind developer that improve this program in his free time.)
- Fixing paste function in the search dialog and in the ID and description of the primer list.
- Fixing zoom function triggered by the drag cap key: the zoomed map is well centered on the dragged region.
New in AmplifX 1.4.4 (Feb 4, 2008)
- Correction of a bug attached to the release 1.4.3 : in the primer sequence, when one wanted to paste or copy with keyboard shortcuts (Apple V or C in Mac or Control V or C in PC world) the appropriate menus were applied but with a prolonged pressure on the two keys : the system passed the second one and the program interpreted it as a base (C for Cytosine or V for � not U � in the IUPAC nomenclature i.e. A or C or G).
New in AmplifX 1.4.3 (Sep 21, 2007)
- [mac] The Mac version is now available as Universal Binary (3x faster onto Mac Intel).
- New interface : the primer’s additionnal informations are at the right of the primer list in the same window : the previous drawer window behaved strangely and the comment field was under used.
- One can now simply select a region into the target sequence and tell AmplifX to design primers to amplify it (Thanks to David Cittaro for this suggestion).
- A double click into the target sequence selects the block with the same case (lower or uper). It’s specialy useful with the previous point.
- Delete key does its job in a primer sequence in the primer list.
- Tab key works to edit the next cell in primer listt.
- One can search into the complement strand in the search dialog
- [win]The Windows XP Interface is less weird ( !) : I have understood what’s the MDI and gave it up (but it’s still far as nice as the Mac version !).
- Limit the scale of the graphic map to avoid losing it when one Maj-clicks without draging
- Save as menu gives a new name with « copy » at the right place (before the extension).
- Correction of the Primer list columns helptags.
- Correction of a bug when importing an AmplifX primer list
- TM and qualty is limited to primers shorter than 100 bp to avoid to kill your computer.
- Comments are not lost when one changes the sequence of a primer.
New in AmplifX 1.4.3 (Sep 19, 2007)
- [mac] The Mac version is now available as Universal Binary (3x faster onto Mac Intel).
- New interface : the primer’s additionnal informations are at the right of the primer list in the same window : the previous drawer window behaved strangely and the comment field was under used.
- One can now simply select a region into the target sequence and tell AmplifX to design primers to amplify it (Thanks to David Cittaro for this suggestion).
- A double click into the target sequence selects the block with the same case (lower or uper). It’s specialy useful with the previous point.
- Delete key does its job in a primer sequence in the primer list.
- Tab key works to edit the next cell in primer listt.
- One can search into the complement strand in the search dialog
- [win]The Windows XP Interface is less weird ( !) : I have understood what’s the MDI and gave it up (but it’s still far as nice as the Mac version !).
- Limit the scale of the graphic map to avoid losing it when one Maj-clicks without draging
- Save as menu gives a new name with « copy » at the right place (before the extension).
- Correction of the Primer list columns helptags.
- Correction of a bug when importing an AmplifX primer list
- TM and qualty is limited to primers shorter than 100 bp to avoid to kill your computer.
- Comments are not lost when one changes the sequence of a primer.