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General Category >> Help and How-to >> Align to reference? https://forum.ugene.net/forum/YaBB.pl?num=1377214101 Message started by Ilya Flyamer on Aug 23rd, 2013 at 6:28am |
Title: Align to reference? Post by Ilya Flyamer on Aug 23rd, 2013 at 6:28am
How can one align a few sequences to one reference sequence in Ugene? So that those sequences don't get aligned to each other at the same time. It should be easy, but I can't find a way to do that.
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Title: Re: Align to reference? Post by Yuriy Vaskin on Aug 26th, 2013 at 12:58pm
Hi there!
In Multiple alignment editor try to use the context menu and "Align sequences to profile with MUSCLE". The reference sequence is the profile. |
Title: Re: Align to reference? Post by Konstantin Okonechnikov on Aug 26th, 2013 at 4:11pm
Hi,
another option would be to use BWA SW. Select menu item "Tools->Align to reference->Align short reads" and then choose BWA SW as alignment algorithm. It is targeted on Sanger-like reads (with length up to several Kbp) and will work fine for long sequences. |
Title: Re: Align to reference? Post by Ilya Flyamer on Aug 30th, 2013 at 10:17pm Yuriy Vaskin wrote on Aug 26th, 2013 at 12:58pm:
It can't work with opened file, can it? It asks to open another file with sequences - will it align only them to the reference sequence or how will it work? |
Title: Re: Align to reference? Post by Ilya Flyamer on Aug 30th, 2013 at 10:18pm Konstantin Okonechnikov wrote on Aug 26th, 2013 at 4:11pm:
Again, it asks to open another files, doesn't it? Are they just not fully integrated on some reason? |
Title: Re: Align to reference? Post by Yuriy Vaskin on Sep 9th, 2013 at 12:00pm
In both cases your sequences must be loaded from a file. Try to export them from the project into a file and then use one of the options to align them.
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