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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 visualisation.
Serial Cloner can read and write DNA Strider-compatible files and also import or export files in FASTA format (or in pDRAW32 format). 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. Numerically select fragments, find restriction sites, ORF or any motif, calculate Tm of selected fragments, %GC or dynamically determine the translation your selection into peptide and calculate the MW using 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 fragment or show single, double or multiple cutter all in the same window.
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 extract a sub-sequence either in a selection or between restriction sites, to create a new PCR-based fragment or synthetic adaptors. shRNA constructions based on pre-defined scaffolds are also automated.
Finally, 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. Finally, Serial Cloner provides an interface to align two sequences using a local algorithm or the BLAST2Seq NCBI server.

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