38 Master direct syntheses list file The master direct syntheses list file is a CSV file that determines the name/number of the next designed direct synthesis sequence. The first line in the file is a header line that does not contain direct synthesis information, but rather just serves to name the columns below. Direct Synthesis Name column fields: The format of the very first direct synthesis name should be "dsNNNXXXXX...", where "NNN" is three characters (e.g. a researcher's initials) and "XXXXX" is the direct synthesis number (the number of Xs, or number of digits allocated for the direct synthesis number, is set by the parameter MASTERPLASMIDNUMBEROFDIGITS; the default is 5, see the description of the j5 parameters file for more information). All other direct synthesis names in the list are completely user-specifiable. The very first direct synthesis name must conform to the format specified above, so that j5 knows how to generate the next direct synthesis name (it just keeps the NNN and increments the direct synthesis number by one beyond the similarly formatted direct synthesis with the greatest direct synthesis number). If there are no direct synthesis entries, j5 will grab the first three characters of the master direct syntheses list file name (e.g. "j5_" in the example below) for the "NNN" characters, and the next direct synthesis will be numbered with "00001" (so the first direct synthesis name would be "j5_00001..." in the example below). Note that header line is still required, even if there are no direct syntheses listed. Alias column fields: The contents of these fields are purely for the benefit of the user, and does not affect the performance of j5 in any way. This information is not generated by j5, but may be added by the user to provide an alternative alias for the direct synthesis name. Contents column fields: The contents of these fields are purely for the benefit of the user, and does not affect the performance of j5 in any way. This information is automatically generated for any new direct syntheses designed by j5 (see SLIC/Gibson/CPEC/SLiCE j5 output for more information). Length column fields: The contents of these fields are purely for the benefit of the user, and does not affect the performance of j5 in any way. This information is automatically generated for any new direct syntheses designed by j5 (see SLIC/Gibson/CPEC/SLiCE j5 output for more information). Sequence column fields: entries are plain text DNA sequences. The contents of these fields are used to check if a given direct synthesis sequence already exists in the master direct syntheses library, before reordering the identical direct synthesis. Here is an example master direct syntheses list file (stylized for clarity; double-click to see enlarged version): In this particular example, the next direct synthesis name would be "dsj5_00002". Here is the actual example direct syntheses list CSV file (j5_directsyntheses.csv):