Profile grid of the PFAM 7 transmembrane receptor (Secretin family) seed alignment associated with a structure of the glucagon-like peptide-1 receptor, PDB 7LCJ. Two residues with 100% type conservation are selected and labeled.

Tool: Profile Grid

Profile Grid shows a condensed view of a multiple sequence alignment in which the rows are the possible sequence characters (residue one-letter codes and gap), the columns are positions in the alignment (as in the standard view of a sequence alignment), and the values in the cells are the prevalences of that type of residue at that position.

Profile Grid is a reimplementation of the viewer developed by Alberto Roca, as described in:

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos. Roca AI. BMC Proc. 2014 Aug 28;8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica):S6.

The values in the ChimeraX Profile Grid are percentages rounded to the nearest integer. A blank cell means that no sequences at all have that residue type at that position, whereas a displayed value of 0 means that some do, but <0.5%. Much like the Sequence Viewer, the Profile Grid tool interacts with any associated structures, and it can include headers above the sequence data.

Opening a sequence alignment file with the open command option viewer grid shows it as a Profile Grid. Multiple Profile Grid windows can be shown at the same time, and they can be manipulated like other panels in ChimeraX (more...).

A Mouse click can interact with the grid cells in either of two ways, as specified near the bottom of the window:

• selects residues – selection of the corresponding residue(s) in any associated structures; if no associated structure has that type of residue at that position, nothing happens. As in the Sequence Viewer, selection of an associated structure residue by any means will be shown as a green outline around the corresponding cell.
• chooses cell – designating Profile Grid cells for subsequent actions, shown with an orange diamond on each chosen cell.

Either way, cell status can be toggled or the cell added to the existing set of highlighted/chosen cells with Shift-click.

[back to top: Profile Grid]

Context Menu

The Profile Grid context menu includes:

• Chosen Cells – actions based on the chosen cells, if any:
  • List Sequence Names – list the names of the corresponding sequences in a separate dialog for copying or saving to a text file
  • New Alignment – open the corresponding sequences in a new window in the specified viewer:
    • Sequence Viewer
    • Profile Grid
• Headers – which headers are shown:
  • Consensus
  • Conservation
  • RMSD – root-mean-square distance among residues associated with a column, based on Cα for peptides, C4' for nucleic acids
  • Save  ▶ [choice of available headers] – save header information to file. Headers are saved to a simple text format that lists the alignment positions and values. See also: sequence header