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Anti-homologous-recombination (and optimization and restriction site checking) sequence analysis program

       While we are optimizing genes from Coffea canephora to BioBrick into our yeast-e coli shuttle vector, we came onto an interesting problem. That Saccharomyces cerevisiae does homologous recombination quite frequently. This problem is significant for us, as our two Caffeine pathway enzymes, XMT1 and DXMT1, are highly similar (initial sequence similarity of 0.8778 through Needleman-Wunsch alignment with 16 stretches of long equivalent sequences >=20bp).
       In order to circumvent this problem, we developed a Java program that aligns sequences, looks for stretches of DNA 20bp or more, then changes codons (in-frame, of course) of the center amino acid to the next most preferable codon (using a yeast codon usage chart). This way, we can get sequences with sharply decreased likelihood of homologous recombination while keeping the amino acid sequence the same. While we are at it, we made the program also check for and remove restriction sites (specified by the user, referenced in a built-in database). The run output of the program is posted in the box to the right!
       As the BioBrick community continues to develop into Saccharomyces cerevisiae and subsequently more complex organisms, we hope that this would provide a useful tool to ease the headache of homologous recombinations affecting experimental results and progress.
       If you would like to test or utilize our program, simply email us at!