OVERFRAG: An overlapping DNA fragments generator for molecular cloning and synthetic biology

DNA synthesis and homologous recombination can be used to simplify molecular cloning and to make synthetic biology easily accessible (M.J. Czar et al., 2009). However, the design of overlapping DNA fragments to construct large molecules is time-consuming and requires verification of several parameters to ensure that fragment synthesis is attainable, given the restrictions found in chemical synthesis of DNA. OVERFRAG is a web-based tool that generates overlapping DNA fragments to assemble either in yeast cells by Gap Repair (H. Ma et al., 1987) or in vitro by (D.G. Gibson et al., 2009) and In-Fusion (B. Zhu et al., 2007) methods. The fragments generated are suitable for chemical synthesis and molecular assembly. Some possible uses include cDNA cloning, design of chimeric antibodies and synthetic biology applications. Web tool is freely available at http://www.each.usp.br/digiampietri/overfrag.