Special Issue: Fact Databases and Freewares] Bioinformatics Tool for Genomic Era: A Step towards the In Silico Experiments - Focused on Molecular Cloning

Abstract

We are making an attempt to perform the molecular biological experiments in silico, one of the most promising alternative means of the biological experiments in vitro. Among the various fields of experiments, this paper is especially focused on molecular cloning, because DNA information is more systematically and exhaustively collected than that of other molecules. There are some advantages in in silico experiments in view of planning molecular biological experiments, usage as lab notebook, educational tool to learn molecular biological experiments. However, performing in silico cloning requires some formulations such as recording of the end shapes of digested products by restriction enzymes or amplified products by PCR. For this purpose, we introduce some extensions to GenBank/EMBL database annotation convention, and incorporate them into existing convention as new feature keys and qualifiers. In addition, features on a DNA sequence are occasionally truncated in the case of amplified products of PCR or digested fragments by restriction enzymes, therefore the annotations about the truncated features should be also formulated. The ambivalent nature of DNA requires frequent changes of the interested strand to and fro, therefore a reverse complementary operation of large size DNA is necessary to be implemented for such software. According to these definitions or data descriptions, we have developed a software tool for in silico experiments, named in silico MolecularCloning, and perform a few of typical molecular cloning experiments on computer, and verified that this approach would be effective.