Introduction to Bioinformatics
Online Course: IBT
Multiple Sequence Alignment
Building Multiple Sequence Alignment
Lec9: A Guide for MSA Coloring
Methods- Protein
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
A Guide for MSA Coloring methods
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Coloring methods for protein alignments
To see the coloring methods available for protein alignments:
1- Open any protein alignment on the Multiple Sequence Alignment Viewer
application home page, for
example, [Link]
Or
2- Upload a file with protein alignment: carbohydrate_kinase_FGGY.aln ,
carbohydrate_kinase_FGGY.aln
Go to the Coloring menu to the right of the Toolbar. Select any of the options and
observe the changes to the display.
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Conservation
This method highlights highly conserved and less conserved amino acid
positions based on the relative entropy threshold of the residue. Only alignment
positions with no gaps will be colored. Red indicates highly conserved
positions, and blue indicates lower conservation.
1 2
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Rasmol Amino Acid Colors
This is the default coloring for a protein alignment in the MSA Viewer. Rasmol
colors are described at Amino acid colors.
1
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Rasmol Amino Acid Colors
- 'amino' renders each of the 20 standard
amino acid residues (as well as Asx and Glx)
in a certain color, along with one additional
color for anything else (including nucleotides,
solvents, and non-amino ligands).
- Some colors are shared by two or more
amino acids with similar properties.
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Residues: amino acid colors
1
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
BLOSUM
"BLOSUM" methods use well-known substitution matrices to display the degree of
match of residues relative to each alignment position/column. When an anchor
row is set, the coloring in the column shows the match score to the residue on the
anchor sequence: blue represents a better match, while green represents a worse
match. When an anchor row is not set, the color reflects the average match over all
the other residues in the column.
1
There are also several coloration methods based on the individual properties of
amino acids. See AAindex for more information about these methods.
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Show Differences
Show Differences highlights differences compared to the anchor
sequence in an alignment. You must set an anchor row to use this
option. Note: Please disregard any coloring when unsetting the anchor
row while still in the "Show Differences" mode.
1
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Frequency-Based Difference (protein)
Frequency-Based Difference compares the residue at a position to
the position/column consensus.
Darker shades of red indicate a further difference from residues in
other rows in the alignment at that position.
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Hydropathy Scale
This coloration method reflects side chain hydropathy, with very hydrophobic in
red to very hydrophylic in blue, corrected for solvation as
in [Link]
1
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Membrane Preference
This coloration method reflects membrane-buried preference parameters as
described in [Link] The color ranges
from red for low membrane preference to green for high preference.
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Structural prediction of membrane-bound proteins
P Argos, J K Rao, P A Hargrave PMID: 7151796 (Free article)
Abstract
A prediction algorithm based on physical characteristics of the twenty amino acids
and refined by comparison to the proposed bacteriorhodopsin structure was
devised to delineate likely membrane-buried regions in the primary sequences of
proteins known to interact with the lipid bilayer.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Shapely Amino Acid Colors
Shapely is another traditional coloring method. Shapely colors are
described at Amino acid colors.
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
'shapely' uses a different set of colors for amino acids (each
one different) and also colors differentially the 6 kinds of
nucleotides.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Signal Sequence
This coloring reflects signal sequence helical potential as
described in [Link]
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Size
The color from red to blue reflects the size of the amino
acid, with red representing smaller side-chains while blue
represents larger side-chains.
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Downloading the Alignment
The Download menu on the toolbar provides options to download a "FASTA
alignment" and export a "Printer-Friendly PDF/SVG" image.
By default, the range will include the viewed range, but the range can be
adjusted in the download dialog. Please refer to this page for more information
about downloading images from the NCBI graphical viewers. If there are hidden
rows, they will not be included in the FASTA alignment or image downloads.
Reference: [Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
(to try in your own time)
Mastering Multiple Sequence Alignment (MSA) in Bioinformatics
Comprehensive flashcards and quiz set from IBT Bioinformatics lectures
by Prof. Ahmed M. Alzohairy
covering MSA tools, interpretation, alignment strategies, and applications.
Difficulty: College 301
MSA interpretation and visualization tools like Boxshade, MSAV, and WebLogo
[Link]
MSA Visualization & Interpretation Tools in Bioinformatics
[Link]
MSA Applications (e.g., Phylogeny, nsSNP, Domain, Structure Prediction)
[Link]
Applications of Multiple Sequence Alignment (MSA) i
[Link]
Troubleshooting and Interpreting MSA Results
[Link]
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Department of Genetics, Zagazig University,
Zagazig, Egypt
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy