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Serial Cloner is a Molecular Biology software that provides tools with an intuitive interface to assists you in DNA cloning, sequence analysis and visualization.
Serial Cloner handles Features/Annotations and now allows to define, import and export, customized lists of Features. User can annotate any sequence portion or use the automatic scan to detect common features. Serial Cloner can read and write DNA Strider-compatible files and also import or export files in FASTA format, VectorNTI, ApE and GenBank files with their features as well as pDRAW32 sequences. MacVector files can
Serial Cloner handles Features/Annotations and now allows to define, import and export, customized lists of Features. User can annotate any sequence portion or use the automatic scan to detect common features. Serial Cloner can read and write DNA Strider-compatible files and also import or export files in FASTA format, VectorNTI, ApE and GenBank files with their features as well as pDRAW32 sequences. MacVector files can
What's New
Version 2.1.3:
- Define user's Feature Collection
- Handling of amino acid-based Features
- Import external Features collections (Serial Cloner Format, Generic table format, ApE format)
- Export Features Collections
- Export Sequences in GenBank format (with Features)
- Directly send BLAST request to NCBI.
- Open degenerate Fasta sequences
- A companion Software to Reset Serial Cloner Preferences in case of problem.
- A companion Software to transform MacVector files to Genbank format compatible with Serial Cloner (from Davide Cittaro)
- Search for a peptide sequence using the Find window.
- Display Features in the Sequence Map window.
- Scan for Features directly in the Sequence Map window
- Create a Feature from a translated sequence
- New "Copy Formatted (Full Seq + Features)" menu to copy the Sequence as formatted in the Sequence Window (Copy More? menu)
- New "Copy as Genbank (Full Seq + Features)" menu (Copy More? menu)
- New Preference to set-up the minimum size of an ORF to be used when searching for all ORFs.
- New Preference to set-up the character size to be used in the Sequence Window
- New Preference to show or not the reverse strand by default in the Sequence Map
- New peptide Features added to Serial Cloner collection for automatic scan (e.g. tags like myc, HA, TEV sites, etc.)
- An pop-up drawing to illustrate cloning using the Build a Construct window (available by clicking the circled i in the window)
- Warns the user when using the Anti-Parallel, Reverse or Complement commands on only a portion of the sequence
- Resizing the Sequence Window is now possible
- Handling of Feature inheritance when sub-cloning (Build a Construct, Gateway)
- List the ORF from the largest to smallest when searching for all ORFs
- Better handling of scrolling when customizing display in the Sequence map window.
- New Keystrokes can be used to select for Particular Enzymes in the Sequence Map (ARROWS, ENTER, ESC)
- Improved parsing of Genbank sequences using the Web Access Window
- Copying/Pasting now tries to keep Features
- Better handling of scrolling of the RE list window
- Better parsing of sequence when pasting a NCBI web page in a Sequence window.
- Better handling of very short (few nucleotides) features.
- Menu modification : a new 'Features' menu has been added and Export functions are grouped together in the File menu
- Menu modification : a 'Copy More...' menu has been created to put together alternative Copy functions
- Scrolling problems in the Sequence Window when selecting a large fragment.
- Detection of Att site when right at fragment extremities.
- Handling of type IIs enzymes
- Handling of Features when using the Anti-Parallel, Reverse or Complement commands
- Setting-up cohesive ends in the shRNA layout window
- A bug that made the HelpWindow appear "randomly"
- Various interface glitches
- Much improved Linux version (although still not officially supported)
Version 2.1.3:
- Define user's Feature Collection
- Handling of amino acid-based Features
- Import external Features collections (Serial Cloner Format, Generic table format, ApE format)
- Export Features Collections
- Export Sequences in GenBank format (with Features)
- Directly send BLAST request to NCBI.
- Open degenerate Fasta sequences
- A companion Software to Reset more...
Requirements
PPC / Intel, Mac OS X 10.4 or later.
PPC / Intel, Mac OS X 10.4 or later.
Serial Cloner User Discussion (Write a Review)
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Serial Cloner is a Molecular Biology software that provides tools with an intuitive interface to assists you in DNA cloning, sequence analysis and visualization.
Serial Cloner handles Features/Annotations and now allows to define, import and export, customized lists of Features. User can annotate any sequence portion or use the automatic scan to detect common features. Serial Cloner can read and write DNA Strider-compatible files and also import or export files in FASTA format, VectorNTI, ApE and GenBank files with their features as well as pDRAW32 sequences. MacVector files can now be imported using a companion software on MacOSX. Genbank/EMBL files can also be read or imported from internet using the included web interface. The included Web interface now also allows to submit BLAST request directly from Serial Cloner Sequence windows
Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. All the tools you need to analyze and manipulate your sequences are available in an all-in-one-window concept. All key functions are accessible through a compact interface. Serial Cloner also lets you build text restriction map and quickly format it to add multi-frame translation or only show single cutters for example. The graphic map of Serial Cloner is really Graphic as you can easily select and extract a feature, a fragment or show single, double or multiple cutter all in the same window. Tex-based Sequence maps are also generated ad now display Features.
Serial Cloner will assist you in setting-up new sub-cloning projects and in preparing the electronic versions of your constructs. In addition to the classical restriction maps - both graphic and text-based - or site usage windows, you will be able to quickly set-up a PCR-based amplification or prepare synthetic adaptors. shRNA constructions based on pre-defined scaffolds are also automated. You can assemble fragments, obtained by PCR, adaptor/shRNA synthesis or simply by graphically selecting fragments between restriction sites. Just select, blunt if you need, and click the Ligate button. An additional interface allows easy Gateway(tm) cloning for both BP and LR reactions. During all these sub-cloning steps, Features present in plasmids and insert will be properly inherited.
Finally, Serial Cloner provides an interface to align two sequences using a local algorithm or the BLAST2Seq NCBI server and extract a consensus, a virtual cutter, a web browser with instant import of NCBI/EMBL entries and a silent restriction map generator. Serial Cloner 2.1 also allows to export GenBank files as well as Fasta-formatted text files. It is also possible to save (or copy in the clipboard) multiple sequences to submit a multi-alignement request to Clustal. A new Copy Formatted option has also been added.
Serial Cloner handles Features/Annotations and now allows to define, import and export, customized lists of Features. User can annotate any sequence portion or use the automatic scan to detect common features. Serial Cloner can read and write DNA Strider-compatible files and also import or export files in FASTA format, VectorNTI, ApE and GenBank files with their features as well as pDRAW32 sequences. MacVector files can now be imported using a companion software on MacOSX. Genbank/EMBL files can also be read or imported from internet using the included web interface. The included Web interface now also allows to submit BLAST request directly from Serial Cloner Sequence windows
Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. All the tools you need to analyze and manipulate your sequences are available in an all-in-one-window concept. All key functions are accessible through a compact interface. Serial Cloner also lets you build text restriction map and quickly format it to add multi-frame translation or only show single cutters for example. The graphic map of Serial Cloner is really Graphic as you can easily select and extract a feature, a fragment or show single, double or multiple cutter all in the same window. Tex-based Sequence maps are also generated ad now display Features.
Serial Cloner will assist you in setting-up new sub-cloning projects and in preparing the electronic versions of your constructs. In addition to the classical restriction maps - both graphic and text-based - or site usage windows, you will be able to quickly set-up a PCR-based amplification or prepare synthetic adaptors. shRNA constructions based on pre-defined scaffolds are also automated. You can assemble fragments, obtained by PCR, adaptor/shRNA synthesis or simply by graphically selecting fragments between restriction sites. Just select, blunt if you need, and click the Ligate button. An additional interface allows easy Gateway(tm) cloning for both BP and LR reactions. During all these sub-cloning steps, Features present in plasmids and insert will be properly inherited.
Finally, Serial Cloner provides an interface to align two sequences using a local algorithm or the BLAST2Seq NCBI server and extract a consensus, a virtual cutter, a web browser with instant import of NCBI/EMBL entries and a silent restriction map generator. Serial Cloner 2.1 also allows to export GenBank files as well as Fasta-formatted text files. It is also possible to save (or copy in the clipboard) multiple sequences to submit a multi-alignement request to Clustal. A new Copy Formatted option has also been added.
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Ycl rated on 19 Apr 2011
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Verity rated on 12 Dec 2010