CSC

Primer Selection

These control the searching for and creation of oligo primers. Together they form the Select Primer functionality of the contig editor. The generate command must be run first. All other commands have undefined behaviour when the generate command has not been run since the last quit command.

select_oligos generate sense forward backward avg_length

Generates a list of oligos suitable for use on the sense strand, within forward bases rightwards of the cursor and backward bases leftwards. Returns the number of oligos found, or -1 for error.

select_oligos next

Picks the next oligo in the list produced by the generate command (or the first if this hasn't been called yet). This remembers the current active oligo number and returns the default template followed by the complete list of templates (including the default) suitable for this oligo.

select_oligos accept template

Adds the tag to the database for this oligo using the named template ("" can be specified here if none is required). Returns a status line containing the template name and the oligo sequence.

select_oligos quit

Frees up memory allocated by generate command.