UGENE Forum - Align to reference?

Aug 23^rd, 2013 at 6:28am

Ilya Flyamer Offline
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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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Reply #1 - Aug 26^th, 2013 at 12:58pm

Yuriy Vaskin Offline
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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.

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Reply #2 - Aug 26^th, 2013 at 4:11pm

Konstantin Okonechnikov Offline
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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.

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Reply #3 - Aug 30^th, 2013 at 10:17pm

Ilya Flyamer Offline
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Yuriy Vaskin wrote on Aug 26^th, 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.

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?

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Reply #4 - Aug 30^th, 2013 at 10:18pm

Ilya Flyamer Offline
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Konstantin Okonechnikov wrote on Aug 26^th, 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.

Again, it asks to open another files, doesn't it?

Are they just not fully integrated on some reason?

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Reply #5 - Sep 9^th, 2013 at 12:00pm

Yuriy Vaskin Offline
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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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