36 Master plasmids list file The master plasmids list file is a CSV file that determines the name/number of the next assembled plasmid. The first line in the file is a header line that does not contain plasmid information, but rather just serves to name the columns below. Plasmid Name column fields: The format of the very first plasmid name should be "pNNNXXXXX", where "NNN" is three characters (e.g. a researcher's initials) and "XXXXX" is the plasmid number (the number of Xs, or number of digits allocated for the plasmid number, is set by the parameter MASTERPLASMIDNUMBEROFDIGITS; the default is 5, see the description of the j5 parameters file for more information). All other plasmid names in the list are completely user-specifiable. The very first plasmid name must conform to the format specified above, so that j5 knows how to generate the next plasmid name (it just keeps the pNNN and increments the plasmid number by one beyond the similarly formatted plasmid in the list with the greatest plasmid number). If there are no plasmid entries, j5 will grab the first three characters of the master plasmids list file name (e.g. "j5_" in the example below) for the "NNN" characters, and the next assembled plasmid will be numbered starting with "00001" (so the first plasmid name would be "pj5_00001" in the example below). Note that header line is still required, even if there are no plasmids listed. NOTE: if the sequences list file contains any sequence files whose display names match the format "pNNNXXXXX" and have the same "NNN" initials used in the master plasmids list file (see immediately above), the next plasmid name "pNNNXXXXX" j5 generates will be one greater than the larger of the highest corresponding numbers in the sequences list and master plasmids list files. For example, if the plasmid naming format derived from the master plasmids list is "pj5_XXXXX", the highest numbered sequence display name beginning with "pj5_" in the sequences list file is "pj5_00010", and the highest numbered plasmid in the master plasmids list is "pj5_00002", then the next plasmid name j5 generates would be "pj5_00011". This behavior assures that any newly generated plasmid names do not match any of the sequence display names in the sequences list file. 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 not generated by j5, but may be added by the user to provide an alternative alias for the plasmid 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 plasmids 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 plasmids designed by j5 (see SLIC/Gibson/CPEC/SLiCE j5 output for more information). Sequence 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 plasmids designed by j5 (see SLIC/Gibson/CPEC/SLiCE j5 output for more information). Here is an example master plasmids list file (stylized for clarity; double-click to see enlarged version): In this particular example, the next plasmid name would be "pj5_00011". Here is the actual example master plasmids list CSV file (j5_plasmids.csv):