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

#       sub topics:
SUB     iupac-codes.hlp

# format described in ../help.readme


TITLE		Design Primers

OCCURRENCE	ARB/Probes/Design Primers

DESCRIPTION     Searches for primer pairs
                within the given physical and biological ranges

                       1. select a species
                       2. open 'PRIMER DESIGN' window
                       3. specify search parameters
                       4. press 'GO' (will open LINK{primer_result.hlp}).

                INIT FROM SPECIES/GENE

                     This initializes the values left and right position and
                     the primer distance with (hopefully) reasonable defaults.

SECTION         Search parameters

                  Left/right position

                    specifies the ranges (where the primer shall reside) using
                    a START position and a given NUMBER OF BASES.

                    The actual sequence data of the currently selected species
                    is examined and the end position of the primer range is
                    set dynamically, such that the range contains the specified
                    number of bases.

                  Primer length

                    Specifies a lower and upper limit for the number of bases the
                    reported primers shall contain.

                  Primer distance

                    Specifies the minimum and maximum wanted
                    distance (in number of bases) between the
                    left and right primer of the reported primer pairs.
                    Optional parameters (ignored if 0).

                  G+C ratio / temperature

                    Specifies minima and maxima for G+C-ratio and temperature of
                    the reported primers.

                  Min. dist to next match of primer

                    If a value above zero is specified, the search accepts
                    primers matching at additional positions, if the distance
                    betweeen the selected position and additional positions is
                    greater than the specified value.

                    A value of zero or below forces all primers to be well-defined (i.e.
                    to match only once).

                    Example:

                             primerposition   100
                             min.dist          50
                             2nd occurrence    30 => distance 70 => primer remains in list
                             3rd occurrence   140 => distance 40 => primer is removed from list

                  Expand IUPAC codes

                    If option is checked, all possibilities of IUPAC codes are permutated
                    when testing for primer matches.

                    When unchecked, primers containing IUPAC codes will not be considered.

                  Max. number of results

                    Limits the number of reported results.

                  G+C- / temperature-factor

                    Allows to weight the impact of G+C vs. temperature while scoring
                    the reported results.



NOTES           all specified positions are from range [0 .. N-1], i.e. when you use a position
                from EDIT4, you need to subtract 1

SECTION         WRITTEN BY

                Wolfram Foerster 2001

EXAMPLES	None

WARNINGS	ARB will crash if you use Primer Design without taking care
		about the estimated memory needed (lower right corner).

BUGS		No bugs known
