Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
Primers database? And Alignment of an abi with DNA ref (Read 9212 times)
Mar 8th, 2011 at 11:33pm

Leduc   Offline
YaBB Newbies

Posts: 2
*
 
Hi,

First, I want to thank you your wonderful software. I'm trying right now to tame it!

First question:
Is it possible to create a primers database that is capable of scanning a DNA sequence to annotate it? In fact, I suppose that the "find groups of annotated regions" can be use for this, but I can not use it... whatever I do, the "search"/"save regions as annotations..."/"Clear results" stay in grayed.
And I want a external Primers database to use it in any projects... if possible!

Second question:
I try to obtain what I can easily do with Ape (a plasmid editor): a abi file can be interactively aligned with a reference DNA sequence. Interactively, because if I observe a problem in the alignment, I can dbl-click on the sequence corresponding to the abi, to see the chromatograph and immeditly check if it is a problem with the quality of the sequence or something else.
Is it possible to obtain a similar function in UGene? I see that I can export the abi file into seq and align this seq with my reference, but like this, it is not easy to check the chromotogram when I find a mismatch...

Thanks again,
Leduc
 
IP Logged
 
Reply #1 - Mar 9th, 2011 at 2:48pm

Konstantin Okonechnikov   Offline
Global Moderator

Posts: 173
*****
 
Leduc wrote on Mar 8th, 2011 at 11:33pm:
Hi,

First, I want to thank you your wonderful software. I'm trying right now to tame it!


Thanks for your kind words! UGENE team are working hard to make the tool useful and easy to use.

Quote:
First question:
Is it possible to create a primers database that is capable of scanning a DNA sequence to annotate it? In fact, I suppose that the "find groups of annotated regions" can be use for this, but I can not use it... whatever I do, the "search"/"save regions as annotations..."/"Clear results" stay in grayed.
And I want a external Primers database to use it in any projects... if possible!


Looks like this question is similar to this feature request. We're working on it! Once there is an availbe solution, I will update this thread. Unfortunately the "Find annotated regions" option will not work here, it only searches for annotations group region in active sequence.

Quote:
Second question:
I try to obtain what I can easily do with Ape (a plasmid editor): a abi file can be interactively aligned with a reference DNA sequence. Interactively, because if I observe a problem in the alignment, I can dbl-click on the sequence corresponding to the abi, to see the chromatograph and immeditly check if it is a problem with the quality of the sequence or something else.
Is it possible to obtain a similar function in UGene? I see that I can export the abi file into seq and align this seq with my reference, but like this, it is not easy to check the chromotogram when I find a mismatch...


Currently capabilities of working with chromatograms are quit limited in UGENE. We're planning to add more features in later releases. However there are some things you can do now:
1) Use Smith-Waterman algorithm on your reference sequence with chromatogram sequence as a query to find alignment.
2) Export annotated region (SW result) as sequence.
3) Add the sequence to chromatogram view and lock the scales. Now you can observe your sequence and aligned part of reference together and correct the errors on the fly.
Refer to this manual section for more details.

 
IP Logged
 
Reply #2 - Mar 9th, 2011 at 5:46pm

Leduc   Offline
YaBB Newbies

Posts: 2
*
 
Konstantin Okonechnikov wrote on Mar 9th, 2011 at 2:48pm:
Looks like this question is similar to this feature request. We're working on it! Once there is an availbe solution, I will update this thread. Unfortunately the "Find annotated regions" option will not work here, it only searches for annotations group region in active sequence.

Thanks for your answers!
Yes, you are right, this is exactly what I want to do. That's fine if it coming soon in UGENE.

Konstantin Okonechnikov wrote on Mar 9th, 2011 at 2:48pm:
Currently capabilities of working with chromatograms are quit limited in UGENE. We're planning to add more features in later releases. However there are some things you can do now:
1) Use Smith-Waterman algorithm on your reference sequence with chromatogram sequence as a query to find alignment.
2) Export annotated region (SW result) as sequence.
3) Add the sequence to chromatogram view and lock the scales. Now you can observe your sequence and aligned part of reference together and correct the errors on the fly.
Refer to this manual section for more details.

Thanks you. It's still a bit too complicated to be really useful in everyday life, but I look forward to future versions of UGEN.

Leduc
 
IP Logged
 
Page Index Toggle Pages: 1