uMUSCLE¶
UGENE contains graphical ports of the Robert C. Edgar’s MUSCLE tool for multiple alignment.
Note
MUSCLE4 is not supported since UGENE version 1.7.2.
The package is integrated completely, so there is no need in extra files for using it. It is possible to run several multiple alignment tasks in parallel, check the progress and cancel the running tasks safely.
Note
The k-mer clustering part of the MUSCLE algorithm was optimized for multicore systems by Timur Tleukenov, Novosibirsk State Technical University.
Aligning with MUSCLE¶
To run the classic MUSCLE use the Align ‣ Align with MUSCLE context menu item in the Alignment editor.
The dialog contains the list of MUSCLE modes: MUSCLE default, Large alignment, Refine only.
Warning
By default UGENE does not rearrange sequence order in an alignment, but the original MUSCLE package does. To enable sequence rearrangement uncheck the Do not re-arrange sequences (-stable) option in the dialog.
One of the improvements to the original MUSCLE package is the ability to align only a part of the model. When the Column range item is selected the region of the specified columns is only passed to the MUSCLE alignment engine. The resulted alignment is inserted into the original one with gaps added or removed on the region boundaries.
Note
To visually select the column range to align, make a selection in the alignment editor first. Then invoke the MUSCLE plugin. Its column range boundary values will automatically match the given selection.
Aligning Profile to Profile with MUSCLE¶
The Align ‣ Align profile to profile with MUSCLE context menu item allows to align an existing profile to an active alignment. During this process the MUSCLE does not realign the profiles, but inserts columns with gaps characters only (‘—’ characters). For example, the alignment in the picture below could be used as a profile:
The same profile after profile-to-profile alignment:
There are two gap columns inserted into the source profile, and two gap columns inserted into the added one. Therefore the profiles columns kept intact and the alignments haven’t been changed.
Note
Aligning a profile to the active alignment you will modify the original alignment file, since it will contain 2 profiles after the operation is completed.
Aligning Sequences to Profile with MUSCLE¶
Another feature provided by the plugin is aligning a set of unaligned sequences to an existing profile. To use this feature select the Align ‣ Align sequences to profile with MUSCLE context menu item.
This option is not available in the original MUSCLE package (v3.7) and is a new functionality for original MUSCLE users. In this mode each sequence from the input file is aligned to the active profile separately and is merged to the result alignment only after all sequences are processed. For example, the alignment in the picture above can be used as a profile again. And the added profile can be used as a set of sequences. The result of such sequences-to-profile alignment is presented on the picture below:
The original alignment is not modified, only columns with gap (‘—’) character can be inserted.
The second profile was considered as a set of sequences and therefore is modified.
Note that if a file with another alignment is used as a source of unaligned sequences, the gap characters are removed and each input sequence is processed independently.
This method is quite fast, for example an alignment of 3000 sequences (1000 bases each) to the existing profile takes about 5 minutes on the usual Core2Duo computer.