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Matchsets
The number of landmarks required will vary depending on the number and quality of
the gels in the MatchSet. Gels with well-resolved spots and little distortion will
require fewer landmarks.
5.5 Automated Matching
Automated Matching dialog
PDQuest includes the ability to match spots with no manual assistance. Unlike
previous versions, you do not have to landmark the images before matching.
This new facility is now the default method used for matching. The previous method
is referred to as "Classic" matching.
Phases of matching
Matching now consists of two phases: Primary matching and Extended matching.
The primary matching phase will make only high-confidence matches. There is a
slider which controls the degree of precision. If you specify high precision, a spot
must be in exactly the expected position based on its neighbors to be matched. If you
lower the precision, the spot is matched even if it is a short distance away from the
ideal position. You will notice that lowering the precision increases the number of
matched spots but may match some spots that should not be matched. The more
reproducible the gels are, the higher the precision setting may be set.
Primary matches are shown in green.
Check the Enable overlapped pH-range matching box to create Cybergels. This will
match gels that only partially overlap. Since this can slow down the matching process
considerably, it is not normally set.
The extended matching phase will make lower confidence matches. The behavior is
similar to lowering the precision in the primary phase, but the matches are displayed
in a different color. This allows you to keep the precision high in the primary phase
and review only the extended matches. The extended match phase allows you to
select several methods, one of which is the classic method. This will use the same
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