Version

Versio 0.5

Description

Among other criteria PRIMER tests oligos for annealing temperature, complementarity to genomic repeat sequences (e.g. Alu) and ability to form primer-dimer. Importantly, PRIMER's annealing temperature calculation is based on thermodynamic parameters (with the base stacking term dominant), and is far more accurate than calculations based on GC/AT ratios. When presented with a short DNA sequence, PRIMER can often design a working PCR assay with known PCR product size without any human guesswork.

While PRIMER was specifically designed to select primers from cloned and sequenced genomic DNAs, many of the tests it performs are useful for selecting oligos for other types of experiments as well, including other PCR applications, oligo hybridization and dideoxy sequencing.

Usage

Type 'primer' at command prompt. No setup commands are needed.

If you want PRIMER to check your sequence for common mammalian repeat requences, save the appropiate file(s) in your working directory using these names:

• human.rep (L1, THE, ALU)

• mouse.rep (B1, B2, L1)

• rat.rep (M-B1, M-B2, RLIN4A)

Note that while PRIMER is available for free use for non-commercial basic research purposes in both academia and industry, PRIMER may NOT be used to design oligos for any commercial purpose whatsoever without specific written permission from The Whitehead Institute. The program along with licencing information can be fetched by anonymous ftp from the Whitehead Institute.

Tips and examples

• Read the original PRIMER manual.

• The program 2primer can be used to quickly format any sequ ence file for primer. Edit the resulting file to specify the correct range.

  Usage: '2primer seqfilename1 > seqfilename2'

• Primer3 at Whitehead Institute.