Database of all genes in Escherichia coli K-12 MG1655 which are not susceptible to restriction enzyme digestion by NdeI and BamHI

Discovery of restriction enzymes that cuts DNA at specific sites ushered in the age of recombinant DNA technology. Although in use for more than 40 years, restriction enzymes remain an essential tool in genetic engineering workflow. Specifically, whether two or multiple fragment assembly, restriction enzymes are enabling tools for cutting DNA, and more crucially, generating the sticky ends that would enable DNA fragments to assemble in desired pattern and orientation. Through the decades, an expanding compendium of restriction enzymes capable of cutting single or double DNA strands as well as generating sticky or blunt ends has been discovered and catalogued. While characteristics of specific restriction enzyme can be obtained from product catalogues, key information concerning whether a gene contains the recognition site of a restriction enzyme remain inaccessible except with a bioinformatic search. Such information on the presence of a recognition site in a gene play a key role in restriction enzyme selection and success in gene cloning or DNA assembly as presence of a recognition sequence of a restriction enzyme would result in the digestion of the gene during the cloning process. Thus, the objective of this database is to provide information on whether the recognition site of two commonly used restriction enzymes, NdeI and BamHI are present in the genes of Escherichia coli K-12 MG1655 (Genbank accession number, NC_000913.3). An in-house MATLAB algorithm was used to parse gene identity and sequence information from the annotated genome sequence of E. coli K-12 MG1655. With the recognition sequence of the two restriction enzymes serving as inputs to the MATLAB programme, the algorithm was capable of cycling through all annotated genes in the E. coli genome and determine if each one contains the recognition sequence of NdeI or BamHI. In cases where the recognition sequence of the restriction enzyme is present in the gene sequence, a value of 1 will be output, otherwise, a value of 0 will be recorded. In short, the database catalogues whether genes in E. coli K-12 MG1655 contains recognition sequence of NdeI and BamHI restriction enzyme. Such information would find use in selecting appropriate restriction enzymes for cloning particular genes from E. coli K-12 MG1655.