What is a good website to check for target specificity of degenerate primers?

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In PRIMER, is it possible to downweight certain taxa in multivariate community datasets to reflect uncertainty around identification??

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How to calculate the annealing temperature of a primer pair?

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Anybody with an idea on how do design specific primers for detecting tomato resistance genes tm-1, TM-2 and Tm2^2?

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What is the ideal efficiency for a qPCR?

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I want to performe MALDI-TOF MS for bacterial identification, I would appreciate it if anyone can tell me the matrix solution preparation protocol ?

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Marwan Al-Maqtoofi

https://eurofinsgenomics.eu/en/dna-rna-oligonucleotides/oligo-tools/primer-design-tools/

https://www.ncbi.nlm.nih.gov/tools/primer-blast/

These are the top sites

Good Luck.

Janhavi Srirangaraj

Dear Marwan Al-Maqtoofi

The primer designing tools you've shared are unfortunately only good for designing and checking for specificity of no-degenerate primer pairs. I was looking to find a tool that is helpful for primers with one or two degenerate bases included in them.

thanks

Shirin Parizad

Hi Janhavi Srirangaraj

Please see if these software/programs are helpful:

1-De-MetaST-BLAST (https://www.protocols.io/view/using-de-metast-blast-ii2ccge)

2-Hyden (http://acgt.cs.tau.ac.il/hyden/)

Good luck