The Protein Multiple Alignment view aligns protein sequences of all orthologs of a single gene annotation (using a variation of the BioMSA algorithm). To open this view, click a gene annotation to display the Annotation Details dialog; navigate to the Orthologs tab, and click the link in the bottom-right corner of the table:

Doing so opens a new dialog:

The top part of the dialog contains alignment options and the list of orthologs; the bottom part contains the actual alignment. You can click the rollout button to expand or collapse each section.

  • Method: Selects the multiple alignment algorithm. 
    • Auto: Automatically selects the best algorithm.
    • Complete: Performs a more complete alignment (using the Needleman-Wunsch algorithm) at the expense of slower performance.
    • Diag: Performs a faster yet less accurate alignment by finding common segments between sequences (called "diagonals"), then running the Needleman-Wunsch algorithm for the missing sequence fragments.
  • Gap penalties: Adjusts the gap open penalty and the gap extend penalty for the alignment algorithm. Higher values penalize gaps more severely; lower values allow for more gaps and/or longer gaps.
  • Query: Lists all the protein sequences to be aligned, in multi-FASTA format:


    You can edit these sequences in-place, or copy/paste your own sequences to be aligned; for example:
  • Orthologs table: Lists the properties of all the aligned sequences. As always, you can click the eyeball button next to an ortholog to open its map and zoom to its gene annotation; you can also click its name to open its Annotation Details dialog directly. Likewise, you can click the Map set or the Map of each ortholog to view their details. Custom sequences (that were manually entered into the Query box, or edited in-place) will not have these links. 

    You can also search and filter this table for items of interest. Items that are hidden in the table are also hidden in the main alignment view:
  • Detailed alignment: Displays the multiple sequence alignment, with color-coded amino acids. The numbers at the top of this plot list the relative offsets of amino acids from the start of the multiple alignment. Click the name of a sequence to open its Annotation Details dialog; as before, custom or manually edited sequences will not have these links. 
  • Alignment overview: Displays the entire multiple alignment at a glance; this "bird's-eye view" makes it easy to find gaps. The box on top of this overview represents the extents of the detailed alignment view; you  can drag it with the mouse to quickly scroll the view: