MenDEL: automated search of BAC sets covering long DNA regions of interest

Motivation Synthetic genomics as a field seeks to synthesize large regions of genomes from the ground up. Such large-scale projects, especially in complex genomes can rely on pre-existing BAC (Bacterial Artificial Chromosome) libraries as starting material to reduce cost. However, choosing BACs that cover long DNA regions, especially those that require many BACs, is a manual, idiosyncratic, time consuming, and error prone process. Automating this work would make the assembly of large DNA constructs more efficient. Results We have developed MenDEL – a web-based DNA design application, that provides efficient tools for finding BACs that cover long regions of interest and allow for sorting results based on multiple user defined criteria - total length, number of BACs, longest BAC. etc. In addition, it enables the user to find a combination of BACs from pre-existing libraries that cover a region of interest not found in any single BAC. Availability and Implementation MenDEL application is available to registered users at , Java code used in the application to find BAC sets is available at ### Competing Interest Statement Jef Boeke is a Founder and Director of CDI Labs, Inc., a Founder of and consultant to Neochromosome, Inc, a Founder, SAB member of and consultant to ReOpen Diagnostics, LLC and serves or served on the Scientific Advisory Board of the following: Sangamo, Inc., Modern Meadow, Inc., Rome Therapeutics, Inc., Sample6, Inc., Tessera Therapeutics, Inc. and the Wyss Institute. David Fenyo is the Founder and President of The Informatics Factory, and serves on the Scientific Advisory Board or consults for: Spectragen Informatics, Protein Metrics, Proteome Software and Preverna.