Tutorial: Performing profile-to-profile and profile-to-sequence MUSCLE alignments

profile-to-profile muscle

Our users can use powerful MUSCLE alignment tool in order to create Multiple Sequence Alignment. But it is also possible to align two existing alignments in UGENE, which is also called „profile-profile alignment“. The operation could be useful for alignments of related sequences and will only insert gap columns into the profiles, thus saving the source alignments. Today we will consider this use case, and one more.

For now, let's open a MUSCLE alignment. We will copy this document to apply another feature to it later, by right-clicking on the document object item and selecting the „Save a copy“ menu item.

To align two profiles, we right-click and activate the context menu, and then select „Analyse“, „Align profile to profile with MUSCLE“ to use MUSCLE sequence alignment tool. In the opened dialog box we select a profile to align. The alignment is done, and we see that there are two gap columns inserted into the first profile, and two gap columns inserted into the second one. Therefore the profiles columns kept intact and the alignments haven't been changed. And there's another option besides aligning two profiles: it's aligning a set of unaligned sequences to an existing profile. In this mode every sequence from input file is aligned to the active profile separately and is merged to the result alignment only after all sequences are processed. The sequence processing order doesn't affect the resulting profile since all the sequences are treated separately. This feature is new for MUSCLE sequence aligner users and is available for UGENE users

Let's activate the saved copy view. We bring up the context menu and select „Analyse“, „Align sequences to profile with MUSCLE“. In the opened dialog box we can select a set of sequences to align or a profile to use as a set of sequences for the sequence aligner. In the latter case all the gap characters from the profile will be ignored. Let's select the same profile we used earlier as a set of sequences. To explore the CLUSTALW-format files we select the corresponding files type. The alignment is done. Again, the source profile is only filled with gap columns and is saved. But the selected alignment was realigned since its every sequence was treated separately. We can switch between the views and thus see the difference between the „profile-profile“ alignment and the „sequence-to-profile“ alignment.

Additional Materials

Documentation page

Youtube video