MUFASA: Multiple fragments assembler for scarless cloning of big genetic constructs.
Overlap-based cloning techniques like Gibson Assembly and Circular Polimerase Extension Cloning (CPEC) have been recently becoming more and more popular. While available software allows rapid overlap design for constructs of conventional size, details of its functioning are not always fully transparent. MUFASA aims not only at facilitating the scarless cloning from the oligonucleotide design to putting the tubes into the thermocycler, but also at designing the fragments themselves in parallel with the overlaps for synthesis of big constructs de novo. Use of multiple overlaps pose a risk of non-specific hybridization and overlap “shadowing”. Such “shadowy places” may be eliminated by thermodynamic sequence optimization of both CPEC primers and fragments of the desired construct.
Overlap optimization algorithms Copyright (C) 2014, 2015 Jakub Bartoszewicz Original implementation Copyright (C) 2014 Jakub Bartoszewicz, Melania Nowicka (Parts Registry connection) Design Copyright (C) 2014 PoznanSoft: Jakub Bartoszewicz, Melania Nowicka, Weronika Krzynowek, Katarzyna Rzosinska
This program uses Primer3 code. See http://primer3.ut.ee/ and: Untergrasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3 - new capabilities and interfaces. Nucleic Acids Research 40(15):e115 Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3 Bioinformatics 23(10):1289-91
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
This program also uses .NET Bio (Apache License, Version 2.0, January 2004, http://www.apache.org/licenses/) and Modern UI for WPF (Microsoft Public License (Ms-PL)). See https://bio.codeplex.com and https://github.com/firstfloorsoftware/mui.
Project funded by the European Regional Development Fund under the Innovative Economy Operational Programme.