Designing Primers: Finding Software to Test Primers

  • Thread starter Monique
  • Start date
  • Tags
    Designing
In summary, the conversation was about finding software to test primers. The speaker used to use the Mac program Amplify, but can't access it anymore. They are looking for other programs, preferably for both PC and Mac. They mention knowing about primer3 from MIT, but not liking it. Eventually, they find the Amplify program on a website and also mention the DNA stryder program, which is only available for Macs. They share a link to a website with freeware for PCs and mention that cellbiol.com is a useful site.
  • #1
Monique
Staff Emeritus
Science Advisor
Gold Member
4,219
67
Now I am looking for some software to test primers with. I always used to eye-ball a sequence, and based on that pick some good looking sequences, put it into the Mac program: Amplify.

This program then visualizes how specific and efficient the priming is on the target sequence by virtual pcr products.

BUT changed workplace, no Amplify.. I am trying to find it on the net though.

Does anyone now other programs which can handle the task? PC or Mac operatable?

I know of primer3 from MIT, but I don't like it..
 
Biology news on Phys.org
  • #2
I have found the Amplify program!

http://www.cellbiol.com/soft.htm

too bad that I don't have a Mac :S

The DNA stryder is really good software too, for sequence manipulations, BUT only for Macs..
 
  • #3
Tadaaaa!

Freeware for PCs
http://www.cellbiol.com/modules.php?op=modload&name=Downloads&file=index&req=viewsdownload&sid=5


Pretty cool site, cellbiol.com
 
Last edited by a moderator:

1. What is the importance of designing primers for experiments?

Designing primers is crucial for experiments, particularly in molecular biology, as they are short pieces of DNA that act as the starting point for DNA replication. They are necessary for amplifying specific DNA segments and are essential for various techniques such as PCR, sequencing, and cloning.

2. What factors should be considered when designing primers?

When designing primers, several factors must be considered, including the melting temperature (Tm) of the primer, GC content, length, and specificity. The Tm should be within a certain range to ensure efficient annealing to the DNA template, and the GC content should be balanced to avoid secondary structures. The length should be between 18-25 nucleotides, and the primer should be specific to the target sequence to avoid non-specific amplification.

3. Can software be used to design primers?

Yes, there is software available that can assist in designing primers for experiments. These software programs use algorithms and databases to optimize primer design based on the target sequence and the desired experimental conditions. They can also check for potential issues such as primer dimers and non-specific binding.

4. What are the benefits of using software for primer design?

Using software for primer design can save time and effort, as it automates the process and provides optimized primer sequences. It also reduces the chances of human error, which can be common when manually designing primers. Additionally, software can provide a more comprehensive analysis and suggest the best primer pair for the experiment.

5. Are there any free software options for designing primers?

Yes, there are several free software options available for designing primers, such as Primer3, Primer-BLAST, and Primer Premier. These programs are user-friendly and have been widely used in research laboratories. However, some advanced features may require a paid subscription or license.

Similar threads

New CRISPR-based tool for find-and-replace editing of DNA
    • Biology and Medical
Replies
2
Views
3K
What programs to learn for IT and web design?
    • Programming and Computer Science
Replies
13
Views
1K
Designing degenerate PCR primers-help
    • Biology and Medical
Replies
4
Views
7K
How can I learn to use Cadence for PCB design?
    • Electrical Engineering
Replies
4
Views
1K
B Golden Ratio in Collatz-like sequences
    • General Math
Replies
1
Views
1K
Job Skills Hoping to find suggestions on time management
    • STEM Career Guidance
Replies
9
Views
960
How to demonstrate the linearity of resistance of water vs. test voltage?
    • Advanced Physics Homework Help
Replies
18
Views
1K
Other NIST SURF Personal Statement Critique
    • STEM Academic Advising
Replies
3
Views
2K
What is the Journey of a Retired Software Engineer?
    • New Member Introductions
Replies
2
Views
198
What is the best beam design for my aluminum tandem axle trailer?
    • Mechanical Engineering
Replies
33
Views
3K

Hot Threads

Recent Insights

Back
Top