#       main topics:
UP      arb.hlp
UP      glossary.hlp

#       sub topics:
SUB     sel_box.hlp

# format described in ../help.readme


TITLE		Potential Probe Targets

OCCURRENCE	ARB/Probes/Design Probes/RESULT

DESCRIPTION	The 'PD RESULT' window is displayed automatically after
		finishing the probe target searching or manually by pressing the
		'RESULT' button of the 'PROBE DESIGN' window.

		The parameters defined by in the 'PROBE DESIGN' window are
			listed in the first few lines of the 'PD RESULT' window.

	
		Description of single display columns:

			Column		contains

			Target		the target sequence of the designed probe
			le		length of designed probe
			apos		absolute 5'-position of the target sites
					(most often targeted position)
			ecol		ecoli-relative position
			qual		a probe quality indicator (see below)
			grps		groupsize (number of perfect hits in target-species)
			G+C		G+C content
			temp		predicted dissociation temperature (4GC+2AT)
			Probe		the designed probe sequence
			
		The numbers of the next columns (from left to right) indicates how many
		non-target species would be detected by this probe if the temperature would
		be gradually lowered ('_' means no hits).

		The columns do only represent virtual temperature shifts and cannot be
		assigned to degree centigrade!

		To write the results to an ascii file press the 'SAVE' button to display
		the 'SELECTION BOX' window.

                The 'Auto match' toggle has the same meaning as in LINK{probematch.hlp}.

SECTION         SORTING

		The probes are sorted by quality. The quality tries to reflect how good
		each probe separates between target- and non-target group.

                Therefore it detects the column COL in the decrease-temparature-list,
                where more than twice as much non-target species would get hitten,
                than mishits (i.e. non-group hits) were encountered by matching the probe.

                Using that column the quality is calculated using the formula

                                                            1000
                        quality = groupsize * COL + ------------------
                                                     1000 + hits[COL]

                    where:
                        * COL is in range 0 .. 19
                        * mishits = probehits - groupsize
                        * probehits = number of hits reported by probe match (zero mismatches)
                        * COL is lowest column where: hits[COL] > 2*mishits
                        * if no column matches the criterion above, COL=19 is used

		Probes with equal qualities are sorted by absolute position and
		then alphabetically. It does not take G+C content, temperature
		or ECOLI position into account.

		It is up to the user to study the list carefully and choose his
		candidates. In our lab we often found the 20th probe was the best.


NOTES		None

EXAMPLES	None

WARNINGS	None

BUGS		No bugs known
