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Feature Database / Scan for feature (Read 6197 times)
May 31st, 2010 at 8:51pm

matt   Offline
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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 - Jun 2nd, 2010 at 12:03pm

Konstantin Okonechnikov   Offline
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matt,
I suppose that this problem could be solved with workflow designer, but need some more details.
could you please clarify your request a little bit?

what particular steps do you perform in your task? (like search for DNA pattern, primer etc.)
could you give an example of query "feature-list" to be executed on a sequence?
 
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Reply #2 - Jun 8th, 2010 at 9:56pm

Sebastian   Offline
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Hi,

I guess matt means auto-annotation of DNA-features (CDS, Promoters, Tags, ...)?
I'm also looking for a way to auto-annotate my Sequences. In detail: scan a dna/aa sequence for known dna and aa patterns (from an annotation db or file) and create annotations for the input sequence.

Should do the same like "Scan for features" in Serial Cloner or "Auto-annotate sequence" in GENtle.
 
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Reply #3 - Jun 18th, 2010 at 3:11pm

matt   Offline
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exactely.
My departement is working with gentle and pdraw32- but i somehow try ugene for my stuff first.
Just as Sebastian said - i meant the auto annotation of DNA features of the Sequence you´re working with.
So for example - if you start working with a quite common vector - you can add features - like promotor regions, selection cassettes, primers etc. once - and than simply "scan" new added sequences for those features instead of annotating each one for itself.

Another example - describing my case (means: beside a feature section for common annotation features (like in the example above - stuff that is used in several labs) it would be great to introduce my own features - which fit to my current project)
In my case it is for a common cloning project where:
1. i start with the gene of interest
2. use the cDNA for creating a vector including parts of it
3. introduce a selection cassette and amplify
4. use the amplified vector for transformation
So on each step several features are the same - so it would make things easier to enter annotations to a list or something similar once - and then simply "scan" your sequence of choice for those.

Hope you got what i mean.
Guess most wishes here lead to features similar to gentle, pdraw, serial cloner, ape and in special probably vectorNti  Wink
 
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