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? Highlight Primers in ab1 tracefile ? (Read 543 times)
Dec 19th, 2020 at 3:13am

grols   Offline
YaBB Newbies

Posts: 1
Hi there,

I want to find primer seqs in ab1 tracefiles I load into ugene. I have a primer library and I also have my primers as fasta...

Here are my questions:

#1 Is there a way to use "Search in Sequence" to find primers in an uploaded ab1 tracefile? (yes, with "Search in Sequence"). But with a large primer set, how do I get the info WHICH primer it is that is found in the trace file? (e.g. the name from the fasta header, or from my primer library)

related to this:

#2 How can I automatically highlight primers (from my primer library) in ab1 tracefiles / chromatograms at upload?

Is this even possible? I tried to find ways myself, but I did not find any documentation on this particular problem.

I know that Genious does stuff like that, but does ugene too?

Thanks a lot. This is a great piece of Software!


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Reply #1 - Dec 21st, 2020 at 12:37pm

Dmitrii Sukhomlinov   Offline
YaBB Administrator

Gender: male
Posts: 54

You can use annotations to mark the found primers. Let's start with the first question:
Yes, you can create annotations using pattern names from the FASTA file. Load the file with primers, click on the "Use pattern name" checkbox and click "Create annotations" (see the attached screenshot 1).
Primers from the Primer Library are supposed to be used with the "In silico PCR" tool, the Primer Library and "Search in sequence" aren't synchronized. So, if you want to find the "Primer Library"'s primers, I suggest you export them into a file and to use the instruction from step 1.

Screenshot_1_002.png (98 KB | 74 )

Best regards,
Dmitrii Sukhomlinov,
UGENE team.
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