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

Abstract

MotivationSynthetic 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. ResultsWe 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 ImplementationMenDEL application is available to registered users at https://mendel-isg.nyumc.org, Java code used in the application to find BAC sets is available at https://github.com/MendelProject/BACFinder