Build your own multiple sequence alignment
The multiple sequence alignment will be built using the proteins
from one or more protein families and a number of protein filters
(currently on a species filter is available).
The first step towards having your own multiple sequence
alignment built is selecting one or more protein families from the
tree. Your are free to select whatever you want, however the quality of
the alignment will best if you select families that are close in the
tree.
Selected protein families appear on the right side of the page, from
where you can remove them if you made a mistake or submit the selected
families which will take you to the next step of the process, selecting
the filters.
After you have selected you protein families, the filter part is
shown. Using these filters you can determine which proteins and wich
residue positions are included in the alignment. More information about
how the filters work and how to use them is provided when you need it.
Note: Due to computational restrictions it is not
possible to generate very large alignments. The upper limit lies around
175,000 residues. This is approximately equivalent to 850 full
proteins, or more if you select specific residues to be aligned. If you
select a bigger set, you will get a warning telling you that you should
limit your selection.
When both the protein families and the filters are submitted, a
submit button appears that will submit the alignment job. Please be
patient, some jobs can take quite a while.
