I would like to design primers for 18S rRNA gene of Cryptosporidium spp. Usually, I use NCBI to design primers. Then I check the primers with multiple sequences alignment in MEGA or design the primers after alignment.
I am looking for any software that can take multiple sequences as input and suggests primers.
I appreciate your kind help.
https://www.thermofisher.com/ma/en/home/life-science/sequencing/sanger-sequencing/pre-designed-primers-pcr-sanger-sequencing.html
You would need to align those sequences first, then look for primer sites. CLC can definitely do both. If you are willing to do some manual processes, Bioedit is great for alignment and shows entropy plots for primer sites.
Hi, The diversity of HIV-1 makes it pretty much mandatory to design primers which can bind to and amplify a wide variety of isolates or lineages by seeking primers that bind in more highly conserved sites in the HIV-1 genome. We thus created some tools to help with this task. The primary tool is here:
https://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html
It works on any input alignment. It does not need to be sequences from any particular organism such as HIV.
Have you checked the ncbi option ? https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?GROUP_TARGET=on
There you can input multiple fasta and exclude specific organisms sequences too.
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