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hbn's Content

There have been 9 items by hbn (Search limited from 22-September 19)


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#151614 Tool / software for oligo analysis (hairpins, dimers etc.)?

Posted by hbn on 05 March 2013 - 02:46 PM in Bioinformatics and Biostatistics

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!



#151593 Tool / software for oligo analysis (hairpins, dimers etc.)?

Posted by hbn on 05 March 2013 - 09:12 AM in Bioinformatics and Biostatistics

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!



#135513 Software to use for Agilent SureSelect probe design

Posted by hbn on 06 June 2012 - 01:08 AM in Bioinformatics and Biostatistics

I am interested in performing target enrichment using the Agilent SureSelect system.
However, the species I am interested in is not a model species. The online eArray tool tells me that I should then use the local software tool eArrayXD. However, I cannot find this software anywhere.
I have contacted Agilent technical support, but they have not been able to help me so far.

Anyone have any experience with this? I would really appreciate any help / advice!



#134443 T7 on single stranded promoter sequence?

Posted by hbn on 12 May 2012 - 01:50 PM in Molecular Biology

Haha, so you are TRYING to do ISH? :P But not on plants, I assume?
Yes, plants are sometimes terrible to work with... I read some papers that this region was highly repetitive but it's worse than I expected! :|
Yes, a lot of target-enrichment kits work this way; with a probe and than 'fishing' out the probe-bound DNA sequences...



#134437 T7 on single stranded promoter sequence?

Posted by hbn on 12 May 2012 - 01:27 PM in Molecular Biology

I guess you are doing ISH? :P
It's quite a repetitive genome (plants are difficult to work with :P ) so making specific probes may also be a challenge.
But still it's not that bad of an idea... Do you have any idea how long the probes and the sheared fragments have to be?



#134433 T7 on single stranded promoter sequence?

Posted by hbn on 12 May 2012 - 01:19 PM in Molecular Biology

No for next-gen sequencing...



#134429 T7 on single stranded promoter sequence?

Posted by hbn on 12 May 2012 - 12:51 PM in Molecular Biology

Jup, highly repetitive :( It's almost impossible to make PCR primers...
But I'm starting from total genomic DNA and I want to perform target enrichment, so I somehow have to select for the region of interest... I guess it's impossible :P



#134425 T7 on single stranded promoter sequence?

Posted by hbn on 12 May 2012 - 12:37 PM in Molecular Biology

blin100,
Thanks for your reply! I thought of that too, but unfortunately, PCR is really difficult in this region, so I'm afraid that will not work... :(
But thanks for your help anyway!



#134341 T7 on single stranded promoter sequence?

Posted by hbn on 10 May 2012 - 07:26 AM in Molecular Biology

I would like to amplify DNA using T7 DNA polymerase, using a primer which has a T7 promoter sequence in front of it.
This means the primer will anneal to the template, but the promoter sequence will not.
Does anyone have any idea if this will work? In other words; does T7 DNA polymerase need double stranded promoter sequence?
Please advise!




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