Google
More docs on the ARB website.
See also index of helppages.
Last update on 25. Nov 2018 .
Main topics:
Related topics:

Design Primers

OCCURRENCE

ARB_NT/Probes/Design Primers

 

DESCRIPTION

Searches for primer pairs within the given physical and biological ranges

  1. select a species (ARB_NT <INFO button>)
  2. open 'PRIMER DESIGN' window
  3. specify search parameters
  4. press 'GO' (will open ´Primer Design RESULT´).

INIT FROM SPECIES/GENE

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

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

 

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