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.

By default, 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.

Typically one would use Profile Grid instead of the standard Sequence Viewer for alignments with very large numbers of sequences. The sequence size threshold for determining the default viewer can be adjusted in the Sequences preferences, although it can be overriden with the open command viewer option (e.g., viewer grid indicates using Profile Grid regardless of the alignment size). 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. Choosing a cell reports in the lower left corner of the window the number of sequences matching that cell.

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

Moving the mouse cursor over a cell reports the column number in the status area at lower right corner of the window, along with the number of associated structure chains (if any) and the residue type(s) in the structure-associated sequences. The residue type(s) in the structures could be different from those in the sequences, but are usually the same since association uses the best match.

Context Menu
Settings

[back to top: Profile Grid]

Context Menu

The Profile Grid context menu includes:

• Choose Cells for Sequence  ▶ [individual sequence names] – choose all cells corresponding to the specified sequence
• Chosen Cells – actions based on the chosen cells, if any:
  • Change in Prevalence... bring up a dialog for showing changes in residue-type prevalences for the chosen subset of sequences relative to all sequences:
    
    • Color other columns by prevalence change: how to color columns without chosen cells
      • Use [N] colors/thresholds (initial default 3) – the fold-change values (coloring thresholds) can be edited directly, and each color changed by clicking its color well and using the system color editor
      • Set colors from palette – change the colors collectively by choosing a palette from the pulldown menu (initial default ^rdbu-3: )
      • Reverse – reverse the order of the colors
      • But color cells with less than [percent] of sequences originally [color] (initial default on, color cells with original full-alignment prevalence <0.5% in )
      • Color transitions:
        • smooth (initial default) – between threshold values, interpolate from one color to the next
        • sharp – change color abruptly halfway between the threshold values
    • Color chosen cells [color] (initial default on and )
    • Color unchosen cells in chosen columns [color] (initial default on and )
    • Revert dialog to the last-used settings
    • Reset dialog to factory-default settings
    • Remove prevalence coloring
    • Apply the current settings
  • 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
• Find Cell Pattern... show dialog to find short stretches of conserved residue types generally or that match a user-specified pattern:
  • pattern [sequence-pattern] – specify a sequence pattern with single-letter amino acid codes, where case is not important. Multiple allowed types at a single position can be given as a set of single-letter characters within square brackets, or as a set of types to exclude within curly brackets, or as a dot (period) to signify that all types are allowed. Each allowed residue type must meet the prevalence criterion. For example, a search for RGD or RGE in three consecutive columns of the alignment could be entered as rg[de], and for CXXC could be entered as C..C, or to disallow cysteines from the second and third positions, C{C}{C}C. However, an important shortcoming is that the search does not allow for variable spacing due to gaps, so that sequences with CXXC will not be detected if the motif is spaced out to more than four columns in the overall alignment.
  • [N] consecutive non-gap cells – find potential motifs in the alignment as N consecutive residues of specific types that meet the prevalence criterion
  • where each cell has [percent] occupancy or higher – prevalence criterion

• 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
  • Individual Sequence as Header  ▶ [individual sequence names]
• Save Image... open browser dialog for saving the currently visible part of the alignment to an image file, with settings:
  • file name and location
  • image file type (several choices, initial default PNG)
  • View spacing (initial default 2) – pixel spacing between the four sections (header names, headers, residue types, and profile grid) that will be composited together to create a single image
  • DPI – image resolution in pixels per inch
• Scroll To Show New Selection If Needed (default on)
• Label Residues... show dialog to label associated structure residues with grids color-coded by residue-type prevalence. The structure residue's type is shown in the label title (along with its number) and with bold font in the grid. Settings:
  • Chains – choose the structure chain of interest
  • Also limit to selected residues, if any – whether to limit labeling to selected residues, or if none are selected, all residues in the chosen chain(s)
  • Use [N] colors/thresholds – specify the coloring palette. The default is from white to blue with increasing prevalence:

    palette 0,white:1,blue  range 0.0,1.0

  • Set colors from palette [palette-name] – choose a built-in palette. Only the ones with the same number of colors as the current number of thresholds will be listed; for example, the rainbow palette will not be listed unless there are exactly 5 thresholds. If any colors are set interactively, the palette name will be shown as custom.
  • Reverse colors – reverse the order of the current colors without changing the number of thresholds or their positions
  • Background color – color to use behind the label text and for filling in empty cells in the last row of the label (default #B4B4B4 )

    Clicking Apply (or OK, which also dismisses the dialog) shows the labels, whereas Close simply dismisses the dialog. Other buttons Revert the dialog to last-used settings, Reset to factory defaults, and show Help in the Help Viewer. See also: sequence grid

• (Mac only) Suppress Horizontal Scrollbar (default on) – hide the horizontal scrollbar to prevent vertical misalignment between rows and their labels; the window can still be scrolled horizontally, e.g., with the trackpad
• Settings... show the Profile Grid preferences to control cell contents

[back to top: Profile Grid]

Settings

Choosing Settings... from the Profile Grid context menu with sections:

• Appearance
• Headers

The settings window can be manipulated like other panels in the ChimeraX interface (more...). See also the Sequences section of the main ChimeraX settings dialog.

Save saves the current settings as preferences, Reset replaces the current settings with the initial “factory” defaults (values shown in bold below), and Restore restores values that were saved previously. The Buttons below... option indicates whether these buttons should apply only to the currently shown section (e.g., Appearance) or to all of the Profile Grid preferences. Although there can be multiple settings windows with different values for multiple Profile Grid windows, there can be only one set of saved preference values.

← Appearance – grid cell contents

• Cell text
  • none – no text, use color only to indicate prevalence
  • count – raw counts
  • percentage (initial default) – counts as a percentage of the number of sequences
• Decimal places for percentages [N] – for percentage values, the number of digits following the decimal (initial default 0)

← Headers – rows of information above the grid of residues (more...)

• Consensus
  • Show initially (initial default off)
  • Hide low-conservation letters (initial default off) – whether to leave the consensus sequence blank at positions where no type meets the High-conservation threshold; otherwise, the most prevalent type at each position will be shown, even if it appears in fewer than half of the sequences, and if several residue types are equally the most common, one will be chosen at random
  • High-conservation threshold (initial default 0.8) – fraction conservation for showing the consensus type as a purple or red capital letter, with red indicating that all sequences have the same type (a fraction of 1.0); consensus types with a fraction below the threshold will be shown as lowercase letters or (if Hide low-conservation letters is on) as blanks
  • Ignore gap characters (initial default off) – whether to exclude gaps from being considered the most prevalent type at a position; regardless of this option, however, gap positions are always included in the denominator for calculating the conservation fraction

• Conservation
  • Show initially (initial default on)
  • Style
    • identity histogram – what proportion of the sequences have the most prevalent nongap character per alignment column. Histogram bar heights are proportional to (M-1)/(N-1), where M is the number of occurrences of the most prevalent residue type at a position in the alignment and N is the number of sequences in the alignment. Thus, if every sequence has a different residue at a given position, the bar height is zero, not 1/N. However, M/N values (not the values used for display purposes) are used for the seq_conservation attribute.
    • Clustal characters – as in Clustal format,
      • * (asterisk) for complete identity
      • : (colon) for strong group conservation
      • . (period) for weak group conservation
      • blank otherwise
    • AL2CO (ALignment 2 COnservation, initial default for alignments with up to 10,000 sequences; for larger alignments, the identity histogram style will be used instead) – more sophisticated options for calculating conservation. Users should cite:

      AL2CO: calculation of positional conservation in a protein sequence alignment. Pei J, Grishin NV. Bioinformatics. 2001 Aug;17(8):700-12.

      Conservation values from AL2CO are in standard deviations from the mean (Z-scores) and can range from –∞ (least conserved) to +∞ (most conserved). For purposes of histogram display only, the values are mapped to bar heights 0-1, with conservation values of zero giving a histogram bar height of 0.5.

      AL2CO parameters:

      • Averaging window (initial default 1) – window width, or how many alignment positions to average in a sliding window. The result is assigned to the central column of the window when the width is odd, the column left of center when the width is even (e.g., the fourth position in a window of 8), with various adjustments at the termini. The authors of AL2CO recommend a width of 3 for motif analyses.
      • Conservation measure – which AL2CO conservation equation to use:
        • entropy-based (initial default)
        • variance-based
        • sum of pairs
      • Frequency estimation method – whether/how to weight the sequences
        • unweighted
        • modified Henikoff & Henikoff
        • independent counts (initial default)
      • Gap fraction (initial default 0.5) – maximum fraction of sequences with gaps in a column for conservation to still be calculated; for example, if the gap fraction is 0.25, conservation values will only be calculated for columns in which at least three-fourths of the sequences have residues
      
      Additional settings if the AL2CO Conservation measure is sum of pairs:
      • Matrix [choices: BLOSUM-30, BLOSUM-35, BLOSUM-40, BLOSUM-45, BLOSUM-50, BLOSUM-55, BLOSUM-60, BLOSUM-62 (initial default), BLOSUM-65, BLOSUM-70, BLOSUM-75, BLOSUM-80, BLOSUM-85, BLOSUM-90, BLOSUM-100, BLOSUM-N, Grantham, HSDM, identity, Nucleic, PAM-40, PAM-120, PAM-150, PAM-250, SDM] – which residue similarity matrix to use
      • Matrix transformation – whether/how to modify the matrix
        • none (initial default)
        • normalization     S'_ab = S_ab / (S_aaS_bb)^½
        • adjustment     S''_ab = 2S_ab – ½(S_aa + S_bb)
  
  
• RMSD – per-column root-mean-square displacement among associated structure residues
  • Show initially (initial default off)
  • Atoms used for RMSD
    • Cα/C4' (initial default) – Cα for peptides, C4' for nucleic acids
    • backbone – peptide N, CA, C, O or nucleic acid phosphoribosyl backbone, not including any hydrogens

  When more than one chain per model is associated with the same alignment, the RMSD calculation uses only the chain that gives the lowest overall RMSD.

• File Markup [Name] (this option will be listed for each GC header read from Stockholm format or a “consensus” sequence, if any, read from MSF)
  • Show initially (initial default on)