To test MAGA with a case study, we prepared a multiple sequence alignment of 34 sequences from the Argonaute protein family, from three subfamilies: AGO, PIWI and CE. CE is an Argonaute Caenorhabditis elegans-specific subfamily, equally distant from the AGO and PIWI subfamilies. We suggest you check which residues are shared between the pairs [CE]+[AGO], [PIWI]+[AGO], [CE]+[PIWI], and all of them together. To do so, we recommend you:|
Now you can analyze the results attending at the color code (red for shared residues in group 1, blue for group 2, purple for group 3).
- Copy the alignment (or upload the file) into the "input alignment" textbox above. Then, click, "Start execution".
- In the results, all sequences are taken as part from the same group. It shows very minimal residues shared between all sequences (in green).
- Group the sequences in three groups, one per subfamily. The ones starting with "CE", place them in group 1; with "PIWI" in group 2; with "AGO" in group 3. And label the groups with "CE", "PIWI" and "AGO" respectively. Then, click, "Execute again!".
Of course, you can tweak the groups as desired, for example by organism. That would mean placing all C. elegans proteins in one group, all Drosophila melanogaster proteins in a different one, and so on.