Serial Cloner This software is a Molecular Biology tool that offers intuitive interfaces to assist you in DNA cloning and sequence analysis.
Serial Cloner 2.6 manages Features/Annotations. It allows you to create, import, and export customized lists of Features. Annotating any sequence can be done by the user. The automatic scan can also be used to identify common features. Serial Cloner can read, write, and import/export DNA Strider-compatible files in FASTA format and VectorNTI, ApE, and GenBank files. It also supports pDRAW32 sequences and their features. The included web interface allows Genbank/EMBL files to be read and imported from the internet. You can also submit BLAST requests directly from Serial Cloner Sequence Windows via the included Web interface. Serial Cloner can open sequences of proteins, align them and reverse-translate them using codon-biais tables. Version 2.6 now allows you to estimate the isolectric points of proteins using a variety of methods.
Simple interfaces and powerful graphical tools make it easy to analyze and construct your sequences. In a single window, all the tools you need for analyzing and manipulating your sequences are at your disposal. The interface is compact and allows you to access all key functions. Serial Cloner allows you to create a text restriction map, format it quickly to add multi-frame translation, or show only single cutters, and so much more. Serial Cloner's graphic map is very graphic. You can select and extract a feature or a fragment, or show single, double, or multiple cutters all within the same window. Also, text-based Sequence maps can be generated and display Features. Serial Cloner can scan for sequence Features and annotations in the sequence and in the Graphic Map. You can add features to protein sequences, and they will be inherited from DNA after translation (using a chosen genetic code).
Serial Cloner will help you set up new sub-cloning programs and prepare electronic versions of your constructs. You will be able quickly to set up a PCR-based amplification and prepare synthetic adaptors. Automated shRNA constructions are possible based on pre-defined scaffolds. You can also assemble fragments using PCR, adaptor/shRNA synthesizer or simply by selecting fragments between restriction sites graphically. Simply select the desired fragments, or blunt them if necessary, and click on the Ligate button. Gateway(tm), a second interface, allows for easy Gateway(tm), cloning of both BP or LR reactions. All sub-cloning steps will allow features in insert and plasmids to be properly inherited.
Serial Cloner allows you to align two sequences using either a local algorithm, or the BLAST2Seq NCBI service and extract a consensus. The aligned sequences can be viewed with their features. You can also access a virtual cutter, a web browser that allows you to import NCBI/EMBL entries instantly and a silent restriction mapping generator. Serial Cloner allows you to export GenBank files and Fasta-formatted text files. Multiple sequences can be saved to the clipboard and copied to Clustal. You can also copy sequences in a formatted and unformatted manner in the clipboard.