Cloning experiments are routinely performed in laboratories worldwide. The starting point of any cloning experiment is in the proper and efficient design and selection of inserts and plasmids. Planning a cloning experiment used to be done on paper. Now, software has allowed this endeavor to be performed on the computer, offering several helpful features. It makes planning for the biochemist and molecular biologist very easy!
I use the Redasoft Visual Cloning™ software for designing all my constructs for cloning experiments. To begin with, this software is extremely user-friendly and does not require extensive training. I very much appreciate the beautiful graphical interface. I only need to import the file containing the sequence of the DNA segment and the software automatically generates a map from the sequence. I can also import the DNA sequence from the clipboard. Importing of sequences from other formats is also supported. For example, GenBank files for vectors can be directly imported to get a vector map. In these files, only the sequence of DNA is automatically read by the software and other details of the sequence provided in the file are used to label the DNA segments. Sequences from NCBI and EMBL can be directly ‘picked-up’ by this software. The software can also import sequences using the Redasoft search engine. The Redasoft ResearchNet feature uses GenBank at NCBI and EMBL (Sequence Retrieval System) as default sites to import sequences; additional websites can be added to the ‘Favorites’ list and can be included while searching.
Once I import the sequence from any of the above sources, I can use it for a whole series of analyses. The most frequent operation I carry out with this software is to analyze the DNA sequence for the presence of restriction sites and open reading frames. The software uses REBASE for maintaining its restriction enzyme database. A series of restriction sites can be detected by using the custom enzyme sets provided in the software. This dataset can be edited as needed and additional enzymes that one needs to use for a particular experiment can be added. I also use this software extensively for designing primers. I can carry out complete cloning experiment in silico to confirm whether the final product I obtain is the one I desire, before actually starting the experiment on my workbench. This saves me a lot of time and money by helping me to avoid wasting time and chemicals. I can also use this software for carrying out multiple sequence alignments – the results are comparable to those obtained from online alignment programs.
This software also allows for the preparation of publication-quality vector maps in no time! Several parameters can be changed during the generation of these maps, including size, shape and color of the designed vectors. However, since the size (in basepairs) is determined by the length of the DNA sequence that is provided as an input, this cannot be manipulated. If I desire a larger map, I add in bases in the region I wish to expand out, and I obtain the plasmid map of my desired dimensions. I can obtain linear or circular maps, although I prefer the circular ones. The generated vector map can be directly exported in different formats (.bmp, .jpeg, .tiff, .eps, etc.), different resolutions and different color shades (RGB/CMYK/black-and-white/grayscale). I usually use the .tiff format, as this is the required format for most journals. The maps can also be directly printed on a printer or as a .pdf. I can also save the maps in the Redasoft format for future editing.
I find that the software is easy to run and does not use up a lot of RAM except while analyzing the DNA segment for restriction enzyme sites or when performing an alignment. It does not take up a lot of hard disk space and does not require a high-end computer. Even more, the software is inexpensive and free updates are always made available on the website! I can also submit sequences imported to the software for online BLAST searches. Overall, I find that this software answers all my requirements for designing cloning experiments and for generating excellent plasmid maps.