Polymerase Chain Reaction is widely held as one of the most important inventions of the 20th century in molecular biology. Small amounts of the genetic material can now be amplified to be able to a identify, manipulate DNA, detect infectious organisms, including the viruses that cause AIDS, hepatitis, tuberculosis, detect genetic variations, including mutations, in human genes and numerous other tasks.
Now I want to design primers for detection of cancer cells apoptosis by myself, and need help to guide me for a good soft ware. TQ
Hello,
I suggest you to use primer-BLAST of NCBI. It is user-friendly.
Regards
http://www.ncbi.nlm.nih.gov/tools/primer-blast/
prime3 is also a nice option. otherwise as suggested NCBI's tool for primer design is kool...
Primer Blast, Primer 3, IDT are free tools. while CLC and DNA star can also be used, if available.
Hi Rahman
I agree with the suggestions. If you want to design primers for qPCR use PRIMER3plus and if you want to do some more sophisticated things like cloning with restriction enzymes I will advice you to use Perfect-primer from Invitrogen. Best luck.
Here they are the links
PRIMER3plus
http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi/
Oligo-perfect
https://tools.lifetechnologies.com/content.cfm?pageid=9716&icid=fr-oligo-6?CID=fl-oligoperfect
There are several software and online tools available for primer design. The best way to do so is the use of paper and pen and believe it will give the result (primers) without any difficulties. You can then use online tool to evaluate primers as per your need.
The best tool you can find -
https://tools.lifetechnologies.com/content.cfm?pageid=9716&icid=fr-oligo-6?CID=fl-oligoperfect
I aslo recommend CLC workbench. I double check my primers with perlprimer.
I think you can use online program like Primer3 or stand alone program like Fast-PCR.
Article FastPCR © : Useful free software for molecular biologists Program
I think for studying analytic aspect like to detect something presence of some organisms, or studying gene expression the online programs like primer 3, but for checking the quality of a particular primer set for using specific purpose software like Oligo is very helpful. But unfortunately it is not free available...
I suggest you to use the primer 3 for designing any kind of primers. If you know how to design the primer by manually, After designing the primer, you may use the ITD website for primer analysis.
The best tool you can find -
http://simgene.com/Primer3
http://www.premierbiosoft.com/primerdesign/
http://www.oligo.net/
http://www.ncbi.nlm.nih.gov/tools/primer-blast/
http://www.genscript.com/cgi-bin/tools/primer_genscript.cgi
http://molbiol-tools.ca/PCR.htm
http://biotools.umassmed.edu/bioapps/primer3_www.cgi
http://www.dnastar.com/t-sub-solutions-molecular-biology-primer-design.aspx
https://tools.lifetechnologies.com/content.cfm?pageid=9716&icid=fr-oligo-6?CID=fl-oligoperfect
https://www.idtdna.com/pages/scitools
I offen use Gene tool software for designing and Primer3 is also good. NCBI also allows you primer designing online but its better go for softwares.
Actually Gene tool software allows primer designing along with other additional genetic tools.
Hi, I think PerlPrimer is one of the best out there: http://perlprimer.sourceforge.net/index.html
It is available for all OS (Win, Linux and Mac). It also has an option to directly blast your selected primers using the NCBI Blast server.
Even though our team has developed a primer designing software for a specific application (exon-junctions), and compiled most primer-designers in one place (see link below), I always preferred manual primer designing or manual confirmation of primers designed by software.
www.startbioinfo.com
Primer3 is TVE best. Most of the rest software are based con Primer3.
For normal PCR you can opt for Primer 3 and OLIGO 7. You can also try for MethPrimer.
I"d prefer the followings:
primer 3
Vector NT
DNAmann
After your get primer pairs, it is always smart to blat your primer and check their specificity.
Thank you very very much for all your kind contributions, that is really appreciated. Regards
FastPCR is a good software as well: http://primerdigital.com/fastpcr.html
Dear Rahman,
vector nti is great but it is not free. Gene Runner and gene script would do it for me but i will also suggest that you should be checking the prmers manually too and i would recommend it as an extra skill because it gives you a better understanding of what you design.
Best wishes,
Nikos
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&ved=0CCwQFjAC&url=http%3A%2F%2Fsimgene.com%2FPrimer3&ei=QjN0VYu8NIGsUbmqgYAP&usg=AFQjCNF2_gap-8uakXrOmzBjVGT4ZZY1_w&sig2=RcvBJqAmzpnw9GTqMxKCYQ&bvm=bv.95039771,d.ZGU&cad=rja
I also used Genome Compiler. Really nice to use and they made the user experience better than any other program that I previously used.
www.genomecompiler.com
use Primer 3 or NCBI primer BLAST tool best tool mean time easy way.......
Primer 3 for regular conventional primer
QuantPrime for real time quantification primers
there are lots of options.i suggest oligo 7. gennerunner .ncbi primer primer 3. allele id. genious. perl primer and...
here is a list of 13 Free PCR Primer Design Programs
https://toptipbio.com/free-primer-design-programs/
i hope this would help
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