SUMO - Sequence logo



WikiPedia explains:

In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).[1] A sequence logo is created from a collection of aligned sequences and depicts the consensus sequence and diversity of the sequences. Sequence logos are frequently used to depict sequence characteristics such as protein-binding sites in DNA or functional units in proteins.

Select SUMO main menu | Utilities | Sequence logo



Enter a set of ALIGNED sequences:


Paste a set of aligned sequences from clipboard ( Clipboard =< text box  butto nor drag a multiple alignment file from Windows' file explorer into the Sequence text box.

Click the  Process  button to generate the Sequence logo:



Copy the graph to Clipboard or save as image file.

SUMO extracts a "majority" sequence from the multiple aligned sequences, taking the maximal abundant residue (i.e. character top in residue stacks) at each alingment positon. Kind of a "maximum intensity projection".
The resulting sequence is shown in Info tab-sheet, and may be copied from there:












Customize the graph

Click the Tool-button to view the tool-box:


Font Size Change the font size.
At present, minimum height/width of a character is limited to at least 10 pixels to allow readability. Click  Apply  button.


Residue numbering
Define the interval at which residure numbers are shone on x-axis.
"1" for every residue, "5" for every fith residue ...

Offset
Maybe you want to indicate the offstream residues relative to a certain feature.
The resdiues until OFFSET are counted negative, numbers at offset start with 1:


Color scheme Select different color schemes to visualize certain - conserved - properties of the sequences (e.g. hydophobity of amino acids in protein alignments).

Residue Colour Schemes
A C G T U I X R Y N W S M K B H D V
Nucleotide
Purine/Pyrimidine

Protein Colour Schemes
A R N D C Q E G H I L K M F P S T W Y V B X Z
Hydrophobicity1
Helix Propencity2
Strand Propencity2
Turn Propencity2
Buried Index3
Clustal4
Zappo5
Taylor6
GECOS Flower7
GECOS Blossom7
GECOS Sunset7
GECOS Ocean7
  1. Residues are colored in respect to their hydrophobicity.
    Hydrophobic-red, hydrophilic-blue.
    Kyte J, Doolittle RF.
    A simple method for displaying the hydropathic character of a protein.
    (1982) J Mol Biol., 157, 105-132
  2. Preference of residue to form a α-helix, β-fold, bend
    Levitt M. (1978)
    Conformational preferences of amino acids in globular proteins.
    Biochemistry, 17, 4277-4285
  3. Relativ to the frequency of occurrence inside globules
  4. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994)
    CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice.
    Nucleic Acids Research, 22:4673-4680.
    - Hydrophobic (A,F,I,L,M,V,W) - Negative charged (D,E) - Positive charged (K,R) - Polar (S,T,Q,N) - Cysteine (C) - Glycines (G) - Proline (P) - Aromatic (H,Y)
  5. Zappo:
    Residues are coloured according to their physicochemical properties as follows:
    - Aliphatic/hydrophobic (I,L,V,A,M)
    - Aromatic (F,W,Y)
    - Positive (K,R,H)
    - Negative (D,E)
    - Hydrophilic (S,T,N,Q) - Conformationally special (P,G) - Cysteine (C)
  6. Taylor WR. (1997)
    Residual colours: a proposal for aminochromography.
    Protein Eng., 10, 743-746
  7. Color schemes basesed on AA-replacement matrix BLOSUM62
    P. Kunzmann, B. E. Mayer, K. Hamacher
    Substitution matrix based color schemes for sequence alignment visualization
    BMC Bioinformatics, vol. 21, pp. 209, May 2020. doi: 10.1186/s12859-020-3526-6
    - Flower: Light color scheme
    - Blossom: Light color scheme with high contrast, depicts symbol similarity worse than flower
    - SunSet: Red-green color vision deficiency adapated
    - Ocean: Blue shifted, light color scheme


Modify a color scheme, by changing individual residues' color.
- Select a Residue character from the Symbol drop down list.
- Click the  ...  button to open a color picker.


Save the modified color scheme as text file
#SUMO_SequenceLogo_ColorScheme
-	rgb(192,192,192)
A	rgb(240,240,240)
C	rgb(128,128,128)
G	rgb(72,72,72)
T	rgb(0,0,0)
R	rgb(5,5,5)
N	rgb(5,5,5)
D	rgb(192,192,192)
Q	rgb(0,0,0)
...


Load a color list, with the above format.


Show residues as:











Decorations

To highligth certain regions in the Sequence Logo you may place rectangles, top or bottom lines over the logo:

Go to Info tab sheet and type a decoration command:

deco.add=type=frame;start=5;stop=10;pen.color=red;pen.width=5;

will place a red box around residues 5-10 using 5 pixel wide stroke.

Object command
type=rect
type=bottomline
type=topline
Plot a rectangle, line on top or bottom
of the sequence region, respectively
Default= rectangle
start=xxfirst residue, where to start the rectangle/line
REQUIRED
stop=xxlast residue, where to start the rectangle/line
REQUIRED
pen.color=colorthe color for the rect/line:
- red,green,blue,yellow,navy,maroon,purple,teal,olive,
aqua,lime,fuchsia,black,gray,silver,white
- any color: rgb(rrr,ggg,bbb), e.g. rgb(255,0,0) = bright redy
Defaultb= black
pen.width=xxwidth of line stroke in pixel
Default=3

You may connect multiple decoration objects with " && " in a single line.

deco.add=type=frame;start=5;stop=6;pen.color=red; && type=frame;start=9;stop=10;pen.color=red; && type=bot;start=7;stop=8;pen.color=maroon; && type=top;start=1;stop=4;pen.color=black

Would generate the decoration in the example image above.


Commands
decoration.add=add a single (or multipe) objects
decoration.listList all defined decoration objects
decoration.clearRemove all defined decoration objects
decoration.delete=xxRemove decoration object xx

To show the graph with newly defined decorations, click  Process  button.