Master oligos list file

The master oligos list file is a CSV file that determines the name/number of the next designed oligo. The first line in the file is a header line that does not contain oligo information, but rather just serves to name the columns below.

Oligo Name column fields: The format of the very first oligo name should be "NNNXXXXX...", where "NNN" is three characters (e.g. a researcher's initials) and "XXXXX" is the oligo number (the number of Xs, or number of digits allocated for the oligo number, is set by the parameter MASTEROLIGONUMBEROFDIGITS; the default is 5, see the description of the j5 parameters file for more information). All other oligo names in the list are completely user-specifiable.

The very first oligo name must conform to the format specified above, so that j5 knows how to generate the next oligo name (it just keeps the NNN and increments the oligo number by one beyond the similarly formatted oligo with the greatest oligo number). If there are no oligo entries, j5 will grab the first three characters of the master oligos list file name (e.g. "j5_" in the example below) for the "NNN" characters, and the next oligo will be numbered with "00001" (so the first oligo name would be "j5_00001..." in the example below). Note that header line is still required, even if there are no oligos listed.

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 oligos designed by j5 (see SLIC/Gibson/CPEC/SLiCE j5 output for more information).

Tm 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 oligos designed by j5 (see SLIC/Gibson/CPEC/SLiCE j5 output for more information).

Tm (3' only) 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 oligos 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 oligo sequence already exists in the master oligo library, before reordering the identical oligo.

Here is an example master oligos list file (stylized for clarity, click here to see enlarged version):

In this particular example, the next oligo name would be "j5_00032".

Here is the actual example master oligos list CSV file (j5_oligos.csv):