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I am having some trouble and I need your help (Read 1532 times)
Sep 27th, 2019 at 7:52pm

Celena9x   Offline
YaBB Newbies

Posts: 1
*
 
i searched - but couldn´t find.

Let´s say i am always working with plasmid or DNA which contains several primer binding sites, which i use regulary (for example a primer binding in a selection cassette).
Is it possible to load a dna sequence and scan it for particular features?
Or even create and extend that feature list (like a group with common feature, a group for features appearing in lab-project x):?

is this possible somehow or do i have to enter new features for each new project???
 
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Reply #1 - Sep 30th, 2019 at 2:06pm

Olga Golosova   Offline
YaBB Administrator

Posts: 338
*****
 
For a single sequence:
* Save all sequences you'd like to search for into a FASTA file like this:
    Quote:
   >pattern1
   ACACGT
   >pattern2
   ACGAAA
   

* Open the sequence (e.g. a plasmid) in the UGENE Sequence View.
* Open the "Search in Sequence" tab on the Options Panel. The quickest way to do it is to use Ctrl+F hotkey (or Cmd+F on macOS).
* Check "Load patterns from file" and browse for the FASTA file.

You should now see the number of found results below. And you can save the results by clicking the "Create annotations" button. If you additionally check "Use pattern name" option in the "Annotation parameters" group, the sequences names in the FASTA file will be used to name the result annotations.

If you'd like to analyze several plasmid sequences at once, you may run a workflow that will do the job, see e.g. "Find pattern" sample workflow. Feel free to ask additional questions, if any.
 
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