PrimerDigital

PrimersList

analysis of the list of primers, cross and self dimers detection and temperature of annealing calculation

Write or paste your primer sequences to the input field (upper window). The analyzer accepts text and table format (can be copied from an Excel file, for example).
The name and sequence string can be separated with either space or tab, as long as the style is the same for all the primers.
The results will appear instantly in the output fields (lower windows), and update automatically if you make changes to the sequences.  The results can be copied and pasted to other programs (Word, Excel, etc.).

*IUPAC DNA degenerate code is an extended vocabulary of 15 letters which allows the description of ambiguous DNA code. Each letter represents a combination of one or several nucleotides:
B=(C,G,T), D=(A,G,T), H=(A,C,T), K=(G,T), M=(A,C), N=(A,C,G,T), R=(A,G), S=(G,C), V=(A,C,G), W=(A,T), Y=(C,T).
U=Uracil; I=Inosine.

*SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc.Natl.Acad.Sci.USA, 95:1460-1465.


Java application based on FastPCR software and FastPCR compatible.

Java application needs a Java Virtual Machines (Sun) (the Java Runtime Environment (JRE) or complete Java Development Kit (JDK), for programmers only, can be downloaded from java.com).

Contact
Dr. Ruslan Kalendar

Reference apply to all Web Tools update, if you use it in your work please cite:

Kalendar R. 2010 Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analyses.
[http://primerdigital.com/tools/]

Copyright

The copyrights and other rights to the materials on the PrimerDigital website are owned by PrimerDigital.
You are authorized to view the materials at this website only for your internal information purposes provided that you: (i) retain all notices contained in the original materials;
(ii) only use images with surrounding text relating to the images;
and (iii) include the following copyright notice.
These computer programs are protected by copyright law and international treaties. Unauthorized reproduction or distribution of this program, or any portion of it, may be result in severe civil and criminal penalties, and will be prosecuted to the maximum extent possible under law.

No transcoding: you are prohibited from using these softwares with a commercial software or hardware product ("commercial product") whose purpose is to "transcode" or convert application content into an alternate programs. A commercial product is one that directly or indirectly generates revenue for its author and/or publisher.