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.
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?
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!
Haha, so you are TRYING to do ISH? 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...
I guess you are doing ISH?
It's quite a repetitive genome (plants are difficult to work with ) 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?
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
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?