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Can someone recommend me a virtual PCR software?


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6 replies to this topic

#1 Annamolec

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Posted 14 July 2011 - 01:59 AM

Hello,
I am working in environmental molecular microbiology. I am getting strange PCR results with a new primer pair. I would like a virtual PCR software to check the specificity. can someone recommend me one?

Thanks!

#2 Trof

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Posted 14 July 2011 - 07:53 AM

PrimerBLAST. It's not exactly virtual PCR, but it shows you binding on nonspecific templates and a designs primers that are specific.

Our country has a serious deficiency in lighthouses. I assume the main reason is that we have no sea.

I never trust anything that can't be doubted.

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#3 Annamolec

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Posted 15 July 2011 - 12:26 AM

Thanks a lot, but i've already tried, and I can only chek my primers against a txt file. I would like something that permits me to check against the whole database.

#4 Trof

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Posted 15 July 2011 - 02:17 AM

No it doesn't. It checks against the selected database.

On the main page you paste the primer sequences and the original sequence you designed primers for or better an accession number of your sequence. (you can upload FASTA file too, but that doesn't mean it checks only against it).
In the Primer Pair Specificity Checking Parameters you need to select the right organism(s) and database (mRNA, genomic) to check for.
As an alternative, you can use BLASTn to check single primer specifity against selected database, but that won't tell you if it creates a PCR product or not.

Our country has a serious deficiency in lighthouses. I assume the main reason is that we have no sea.

I never trust anything that can't be doubted.

'Normal' is a dryer setting. - Elizabeth Moon


#5 Annamolec

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Posted 20 July 2011 - 11:05 PM

Hi,
Thanks a lot. There is only one more problem. It doesn't recognize degenerated primers. Is it true or is me again?

#6 Trof

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Posted 21 July 2011 - 09:17 AM

I'm afraid it doesn't.

Our country has a serious deficiency in lighthouses. I assume the main reason is that we have no sea.

I never trust anything that can't be doubted.

'Normal' is a dryer setting. - Elizabeth Moon


#7 Su.J

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Posted 09 September 2011 - 04:53 AM

amplix software...it checks ur primer binding, runs a pcr n tells if ur getting ur band of interest!!!:)




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