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General Category >> Help and How-to >> Primers database? And Alignment of an abi with DNA ref https://forum.ugene.net/forum/YaBB.pl?num=1299602016 Message started by Leduc on Mar 8th, 2011 at 11:33pm |
Title: Primers database? And Alignment of an abi with DNA ref Post by Leduc 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! 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 |
Title: Re: Primers database? And Alignment of an abi with DNA ref Post by Konstantin Okonechnikov on Mar 9th, 2011 at 2:48pm Leduc wrote on Mar 8th, 2011 at 11:33pm:
Thanks for your kind words! UGENE team are working hard to make the tool useful and easy to use. Quote:
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:
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. |
Title: Re: Primers database? And Alignment of an abi with DNA ref Post by Leduc on Mar 9th, 2011 at 5:46pm Konstantin Okonechnikov wrote on Mar 9th, 2011 at 2:48pm:
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:
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 |
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