As always, it took longer to release this new version than expected. But at last, it is there with many improvements and bug fixes.

The main enhancement is the possibility to define your own list of Features to be scanned for. A new interface has been developed that also allows to Import/Export Feature Collections.

In addition, Features are now shown of the Sequence Map which was an often requested function. As was the possibility to resize the Sequence Window. I never do but it was clear that most of you wants to. So here it is.

I updated the Manual file that describes Features, I strongly encourage you to read it to get familiar with the new possibilities (like definition of peptide Features, new Copy-Paste, new Export format, etc.).

Also present in version 2.1 are the possibility to directly send BLAST request, to search for a peptide sequence or to expor sequences in a Genbank format.

With Serial Cloner 2.1, I also provide an additional little software that you can use to reset Serial Cloner Preferences. Some (fortunately few) users suffered form Preference File corruption, so I simplified for them the correction of this problem. With the MacOSX version also comes a little drop-in application developed by Davide Cittaro that allows to transform MacVector fles to Genbank. Serial Cloner can then import these files. Please, read the short description that is provided with the software.

Another large list of Additions/Corrections comes with Serial Cloner 2.1 - see below.

Serial Cloner is still distributed as a freeware although you are welcome to support it.

Enjoy,

Franck.

What's new in Serial Cloner 2.1

(see the online help accessible from within Serial Cloner to get more details on the different actions)

- [NEW] Define user's Feature Collection

- [NEW] Handling of amino acid-based Features

- [NEW] Import external Features collections (Serial Cloner Format, Generic table format, ApE format)

- [NEW] Export Features Collections

- [NEW] Export Sequences in GenBank format (with Features)

- [NEW] Directly send BLAST request to NCBI.

- [NEW] Open degenerate Fasta sequences

- [NEW] A companion Software to Reset Serial Cloner Preferences in case of problem.

- [NEW] A companion Software to transform MacVector files to Genbank format compatible with Serial Cloner (from Davide Cittaro)

- [ADDED] Search for a peptide sequence using the Find window.

- [ADDED] Display Features in the Sequence Map window.

- [ADDED] Scan for Features directly in the Sequence Map window

- [ADDED] Create a Feature from a translated sequence

- [ADDED] New "Copy Formatted (Full Seq + Features)" menu to copy the Sequence as formatted in the Sequence Window (Copy More? menu)

- [ADDED] New "Copy as Genbank (Full Seq + Features)" menu (Copy More? menu)

- [ADDED] New Preference to set-up the minimum size of an ORF to be used when searching for all ORFs.

- [ADDED] New Preference to set-up the character size to be used in the Sequence Window

- [ADDED] New Preference to show or not the reverse strand by default in the Sequence Map

- [ADDED] New peptide Features added to Serial Cloner collection for automatic scan (e.g. tags like myc, HA, TEV sites, etc.)

- [ADDED] An pop-up drawing to illustrate cloning using the Build a Construct window (available by clicking the circled i in the window)

- [ADDED] Warns the user when using the Anti-Parallel, Reverse or Complement commands on only a portion of the sequence

- [UPDATED] Resizing the Sequence Window is now possible

- [UPDATED] Handling of Feature inheritance when sub-cloning (Build a Construct, Gateway)

- [UPDATED] List the ORF from the largest to smallest when searching for all ORFs

- [UPDATED] Better handling of scrolling when customizing display in the Sequence map window.

- [UPDATED] New Keystrokes can be used to select for Particular Enzymes in the Sequence Map (ARROWS, ENTER, ESC)

- [UPDATED] Improved parsing of Genbank sequences using the Web Access Window

- [UPDATED] Copying/Pasting now tries to keep Features

- [UPDATED] Better handling of scrolling of the RE list window

- [UPDATED] Better parsing of sequence when pasting a NCBI web page in a Sequence window.

- [UPDATED] Better handling of very short (few nucleotides) features.

- [UPDATED] Menu modification :  a new 'Features' menu has been added and Export functions are grouped together in the File menu

- [UPDATED] Menu modification :  a 'Copy More...' menu has been created to put together alternative Copy functions

- [CORRECTED] Scrolling problems in the Sequence Window when selecting a large fragment.

- [CORRECTED] Detection of Att site when right at fragment extremities.

- [CORRECTED] Handling of type IIs enzymes

- [CORRECTED] Handling of Features when using the Anti-Parallel, Reverse or Complement commands

- [CORRECTED] Setting-up cohesive ends in the shRNA layout window

- [CORRECTED] A bug that made the HelpWindow appear "randomly"

- [CORRECTED] Various interface glitches

- [CORRECTED] Much improved Linux version (although still not officially supported)

A short manual describing Features handling has been updated and added as a pdf file.