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. Find Internal Joins is to avoid finding matches that are entirely contained in Alu segments. 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.
This page is maintained by James Bonfield . Last generated on 2 Febuary 1999.