Tags are used for a variety of purposes and for each function in the program the user can choose which tag types are currently "active". Where they are being used to provide visual clues this will determine which tag types appear in the displays, but for other functions they can be used to control which parts of the sequence are omitted from processing. This mode of tag use is called "masking". For example the program contains a routine to search for repeats, and if any are found, the user needs to know if such sequence duplications are caused by incorrect assembly or are genuine repeats. Once the user has checked a duplication reported by the program and found it to be a repeat, it can be labelled with a REPT tag. If the repeat routine is run in masking mode and with REPT tags active, any segment covered by a REPT tag will not be reported as a match. So once the "problem" has been dealt with it can be labelled so it is not reported on subsequent searches. In addition the tag is available to provide annotation for the completed sequence when it is sent to the data libraries.
A more complicated application of masking is available for two of the other search procedures in the program: (see section Shotgun assembly) and (see section Find Internal Joins). The former is the general assembly function and the latter is used to find potential joins between contigs in the database. Below we describe how masking can be used during assembly and similar comments apply to Find Internal Joins. In the assembly function the user can choose to employ masking and then select the types of tags to be used as masks. Readings are compared in two stages: first the program looks for exact matches of some minimum length and then for each possible overlap it performs an alignment. If the masking mode is selected the masked regions are not used during the search for exact matches, but they are used during alignment. The effect of this is that new readings that would lie entirely inside masked regions will not produce exact matches and so will not be entered. However readings that have sufficient data outside of masked segments can produce matches and will be correctly aligned even if they overlap the masked data. A common use for masking during assembly or Find Internal Joins is to avoid finding matches that are entirely contained in Alu segments.
A further mode related to masking is "marking". Marking is available for the consensus calculation (see section Consensus calculation) and for Find Internal Joins (see section Find Internal Joins). Instead of masking the regions covered by active tags these routines simply write these sections of the consensus sequence in lowercase letters. That is they make it easy for users to see where the tagged segments are. Marking has no other effect.