Features are now visible when aligning locally. Finally, Serial Cloner provides an interface to align two sequences using a local algorithm or the BLAST2Seq NCBI server. An additional interface allows easy Gateway(tm) cloning for both BP and LR reactions. Just select, blunt if you need, and click the Ligate button. Finally, you can assemble fragments, obtained by PCR, adaptor/shRNA synthesis or simply by graphically selecting fragments between restriction sites. shRNA constructions based on pre-defined scaffolds are also automated. 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. Serial Cloner will assist you in setting-up new sub-cloning projects and in preparing the electronic versions of your constructs. Version 2.5 now allows to open protein sequences, align protein sequences and reverse translate proteins using defined codon biais tables. The Collection of Features to be scanned for can be defined and modified by the user, imported and exported. All the features are displayed on the map using user-modifiable colors the features can be manually entered, imported from GenBank or automatically found after scanning by Serial Cloner. 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. Since version 2.1, Sequence Features are visible in the Sequence Map. 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. Numerically select fragments, find restriction sites, ORF or any nucleotide or peptide sequence, 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 2.5, handles Annotations and Features both in the sequence and in the Graphic Map and can automatically scan for sequence Features.Īll the tools you need to analyze and manipulate your sequences are available in an all-in-one-window concept. Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. Import from VectorNTI multi-file format is also supported. Serial Cloner also import files saved in the Vector NTI, MacVector, ApE, DNAstar, pDRAW32 and GenBank formats. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format. Serial Cloner has been developed to provide a light yet powerful molecular biology software to both Macintosh and Windows users. (Most other applications will ignore all sequences past the first, so the behavior may differ slightly).įiles in this column are results from Sanger sequencing, and will contain chromatogram traces along with quality data when imported as an alignment.Serial Cloner has been developed to provide a light yet powerful molecular biology software to its users. When a multi-sequence file is imported, Benchling will automatically split the archive and import each individual sequence into your library. Benchling sometimes tries to guess the file format by extension, so if you ever encounter importer errors and the file extension doesn’t match the table, try renaming the file and then reimporting.įiles in this column are archives that can potentially contain more than one sequence. The easiest way to get these sequences into Benchling is to create a new sequence and then copy and paste in the bases. Format NameĪt the moment, Benchling unfortunately cannot parse out sequences saved as PDF or as Microsoft Word files (doc, docx). The following formats are fully supported in Benchling – the sequence, annotations, and comments will all be directly imported into Benchling. Benchling fully supports these two formats, so when encountering importer errors or trying to import sequences from an unsupported format, a quick workaround is to “save as” to either format as most applications can export either Genbank or FASTA. The most common two file formats are GenBank and FASTA. If you ever run into any problems, please don’t hesitate to ask for help at Overview We’re constantly updating the formats we support, so just try dragging in your files into the importer – our goal is to have the importer “just work” regardless of the file format. Benchling supports a wide range of file formats, including both common and proprietary ones.
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