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bioRxiv · 10.1101/2022.06.26.496179

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

German, S.·Pinglay, S.·Camellato, B.·Fenyo, D.·Boeke, J. D.
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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

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German, S., Pinglay, S., Camellato, B., Fenyo, D., Boeke, J. D.. 2022-06-29. MenDEL: automated search of BAC sets covering long DNA regions of interest. https://doi.org/10.1101/2022.06.26.496179

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