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Pixel Explanation


Pixel provides quality control for alignments. Alignment quality is very important for getting good results from many tools, so Pixel is recommended as an easy way to find alignment errors prior to using a new alignment for subsequent analyses.

Basic or Advanced?

If you are using the tool for the first time, we recommend looking at your pixel image with the Basic settings and color schemes first. Also, if your pixel image "looks weird" or is difficult to view in Advanced, try Basic.


Input can be:


The output of this tool is an image that you can download in several formats. Below we have analyzed a HIV-1 Vif amino acid alignment.

Now an error is introduced into this alignment - one sequence is out of alignment by 1 amino acid, approximately in the center of the alignment. It looks like this using Pixel's default settings. It is visible, but it can be made more obvious by changing the color scheme or scale (see below).


Color scheme

By default, nucleotides and amino acids are all displayed in color. In some cases, errors are easier to identify when different color schemes are used.

Default colors (shown above):
Amino Acids or nucleotides (all) - various colors
Gap - white
Stop codons or frameshifts - red
Unknown residues - black

Matches gray
Amino acids (not matching first sequence) - default colors
Amino acids (matching first sequence) - gray
Gap - white
Stop codons or frameshifts - red
Unknown residues - black

Matches white, mismatches red, indels black
Amino acids (not matching first sequence) - red
Amino acids (matching first sequence) - white
Gap or insertion - black

Jmol "shapely" (Advanced Pixel only)

This is the color scheme used by JMol.

Se-Al (Advanced Pixel only)

These are the colors used to display nucleotides and amino acids in the Se-Al software.


Scale (Basic Pixel only)

To see small errors, set the Scale option to a larger number. Using the default colors for the example above, but setting the scale to 2, we see the error more clearly:

Show differences relative to reference sequence (Advanced Pixel only)

This option provides additional color schemes in Advanced Pixel. Examples of these color schemes are illustrated above ("Matches gray" and "Matches white, mismatches red, indels black"). In the case of "Matches gray", Advanced Pixel will use the chosen color scheme to color the non-gray residues.

Reference sequence (Advanced Pixel only)

This option works in conjunction with "Show differences relative to reference sequence." To select a reference sequence other than the first sequence in the alignment, enter the exact sequence name as it appears in the alignment file.

Plot size (Advanced Pixel only)

These options allow you to choose the pixel size OR the overall plot size of your image. If you choose to "Automatically compute", the program will choose the overall dimensions based on the residue scale. The residue scale option is similar to the "Scale" option in Basic Pixel. You can change your plot size either by changing the residue scale or by setting the dimensions in inches, but not both.

Show sequence names (Advanced Pixel only)

This option will show the sequence names in the pixel image. The default font size is selected automatically, but you can choose it.

Show scale bar (Advanced Pixel only)

When selected, this option will display a scale bar under your pixel image. The height of the scale bar can be adjusted by entering a scale bar size in the blank provided.

Margins (Advanced Pixel only)

You can use this option to adjust the margins on your pixel image.

last modified: Thu Jul 7 11:38 2016

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