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Tool / software for oligo analysis (hairpins, dimers etc.)?

bioinformatics oligo primer design software hairpins

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5 replies to this topic

#1 hbn

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Posted 05 March 2013 - 09:12 AM

Hi all!

I am looking for something very simple, but I haven't been able to find it yet:

A simple software tool (preferrable linux command-line) which can analyze some basic characteristics of oligos / primer pairs, such as hairpins, dimers etc. The only hits I am getting is Primer3, but I have my primers already, so I don't think I can analyze my self-made primers with that, right?

Hope anyone can help!

Cheers!

#2 Trof

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Posted 05 March 2013 - 10:19 AM

Yes you can. Just put your sequences in.
But Primer3 uses it's own scoring system. But one you get familiar with them, it's pretty usable, giving both pair and individual values separately for overal and 3' end.

You can use modified Primer3+ to check individual primer (not pairs), this gives ΔG values for 3' stability.

The best graphical overview probably has Oligo Analyzer, also giving ΔG.

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


#3 hbn

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Posted 05 March 2013 - 02:46 PM

Hi Trof,

Thanks for your reply! But do you mean the stand-alone (command-line) version of Primer3 can do it? Which parameters do you use for your own designed primers? SEQUENCE_LEFT_ something??
Or do you mean the online version?

I know IDT's Oligo Analyzer, which is also good, but I'd prefer a stand-alone (preferably command-line) version.

Cheers!

#4 Trof

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Posted 05 March 2013 - 03:02 PM

I have never used command-line version. Online version can do that.

Does this help?

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 sikander

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Posted 01 May 2013 - 02:04 PM

hii

I used this and this works fine. Try this one. If have any further problem let me know.



http://www.basic.nor.../oligocalc.html

best wishes

#6 memari

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Posted 01 May 2013 - 05:25 PM

http://biocompute.bm.../MFEprimer-2.0/
-----
Babak Memari





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