PrimerDigital


Primers analysis and compatibility




Paste or type the primer or primers sequence(s) at any TAB Editors, the program will immediately show primer characteristics:
length in bases, melting temperature, CG% content, molecular weight, the extinction coefficient (e260), nmol per 1 OD, the mass - µg per 1 OD, linguistic complexity (%) and primer quality (%);
minimal and maximal optimal annealing temperature for unknown PCR products. Tm calculation based on chosen the formula from “Primers Design Options”.

If the primer is self-complementary, the program will show a picture of where this self-complementarity happens. All primers analysed for self-dimers formation and by your wishes primers can analysed with each other for detection cross dimers formation. A self-priming ability will also be detected and shown by the program. When the two primers are forming such a dimer, the program will also show it.

Web Java version for on-line primer test with Tm calculation for normal and degenerated nucleotide combinations based on the nearest neighbour thermodynamic parameters and comprehensive dilution protocol available at WebTols.
Comprehensive analysis of the list of primers with prediction of the oligonucleotides properties, self and cross dimers detection and temperature of annealing calculation is available at jPCR Web Tools.

Primers analyses



Single or list of primers is evaluate by FastPCR for calculation Tm (default or other formula) for normal and degenerated nucleotide combinations, CG content, the extinction coefficient, nmol per OD, the mass - µg per OD, the molecular weight, linguistic complexity (%) and primer quality (%).
All primers analysed for self-dimers formation and by your wishes primers can analysed with each other for detection cross dimers formation.

  • Forward against Reverse (F/R) it is possible selectively analyse primer pair forward and reverse.
For this type of analysis, primers from the same pair must have identical names but finishing using “R or F” (in FASTA format:
>seq1R and >seq1F form a pair).
The name length and structure (including "F" and "R" inside names) are not important.
Moreover, the program is not limited in one unique pair per primers: for one "forward" primer, it can be several "reverse", the same for “reverse” primer.

  • “Show primers Tm for all NN thermodynamic parameters and formulas” – allowed seeing all Tm’s result for all formulas at “Primers Design Options”.

FastPCR


FastPCR