Introduction to Bioinformatics
Online Course: IBT
Multiple Sequence Alignment
Building Multiple Sequence Alignment
Lec5: Interpreting your MSA Using Logos
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Using Logos
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
- Logos are a terrific way to generate high-
impact pictures from MSA
- logo Figure is a representation of the alignment.
- Notice how the conserved amino acids (e.g
cysteines) stick out, indicating regions of
potential biological importance.
Claverie J, Notredame C (2007). Bioinformatics for Dummies (2nd Edn). Wiley publishing, Inc. 436 pp.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
When looking at a sequence logo, you can consider the
following elements:
- Each position corresponds to a column in the multiple
alignment.
- The total height of a logo position depends on the
degree of conservation in the corresponding multiple
alignment column.
Claverie J, Notredame C (2007). Bioinformatics for Dummies (2nd Edn). Wiley publishing, Inc. 436 pp.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
- Very conserved alignment columns give you high logo
positions.
- Positions that contain a very heterogeneous mixture of
symbols yield low logo positions.
- The size of each letter in a logo position depends on
how frequent this letter is in the column.
- The top letter is always the most frequent in the
column.
Claverie J, Notredame C (2007). Bioinformatics for Dummies (2nd Edn). Wiley publishing, Inc. 436 pp.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
- Logos make sense only if you have a nice block with a few
highly conserved positions surrounded by highly
degenerated positions.
- There is a handy utility on the Web that identifies blocks
within your multiple alignments and turns each of them into a
logo.
- blocks.fhcrc.org./blocks/process_blocks.html
Claverie J, Notredame C (2007). Bioinformatics for Dummies (2nd Edn). Wiley publishing, Inc. 436 pp.
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
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Examples
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Catobolite Activator Protein (CAP)
The helix-turn-helix motif from the CAP family of homodimeric DNA binding proteins.
CAP (Catabolite Activator Protein, also known as CRP for cAMP Receptor Protein) is a
transcription promoter that binds at more than 100 sites within the E. coli genome.
Residues 1-7 form the first helix, 8-11 the turn and 12-20 form the DNA recognition
helix. The glycine at position 9 appears to be critical in forming the turn. Positions 4,
8, 10, 15 and 19 are partially or completely buried, and therefore tend to be populated
by hydrophobic amino acids, which are colored black. Positions 11-14, 17 and 20
interact directly with bases in the major groove and are critical to the sequence
specific binding of the protein. The data for this logo consists of 100 sequences from
the full Pfam alignment of this family (Accession number PF00325). A few sequences
with rare insertions were removed for convenience.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
The two DNA recognition helixes of the CAP dimer insert themselves into into cThe two
DNA recognition helixes of the CAP homodimer insert themselves into consecutive turns of
the major groove. Several consequences can be observed in this CAP binding site logo.
The logo is approximately palindromic, which provides two very similar recognition sites,
one for each subunit of the dimer. However, the binding site is not perfectly symmetric,
possible due to the inherent asymmetry of the operon promoter region. The displacement of
the two parts is 11 base pairs, or approximately one full turn of the DNA helix. Additional
interactions between the protein and the first and last two bases occur within the DNA minor
groove, where it is difficult for the protein to distinguish A from T, or G from
C\cite{Seeman76}. The data for this logo consists of 59 binding sites determined by DNA
footprinting. Robison, K., McGuire, A. M., Church, G. M. A comprehensive library of DNA-
binding site matrices for 55 proteins applied to the complete Escherichia coli K12 genome.
Journal of Molecular Biology (1998) 284, 241-254.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
E. coli Transcription Factor Binding Sites
The following logos (along with the CAP logo above) display a selection of E. coli
transcription factor binding sites determined by DNA footprinting. This data has been
collated in the DPInteract database and has been used to search for additional binding
sites within the E. coli genome.
- LexA repressor is closely related to CAP, and has similar DNA protein interactions.
- H-NS: Histone like, nucleoid-associated DNA-binding protein.
- DNA biosynthesis initiation binding protein.
- Arginine Repressor.
Robison, K., McGuire, A. M., Church, G. M. A comprehensive library of DNA-binding site matrices
for 55 proteins applied to the complete Escherichia coli K12 genome. Journal of Molecular Biology
(1998) 284, 241-254.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
E. coli Promoters (Transcription Start Signals)
In prokaryotes the DNA sequence just upstream of the transcription start point
contains two important conserved regions. The first such region is centered at
around 35bp upstream and is involved in the initial recognition of the gene by
RNA polymerase. The second region, sometimes referred to as the Pribnow
box, is centered at about 10bp upstream. The typical separation between the -
35 and -10 sites is 15-18 bp. See baseflip: Strong Minor Groove Base
Conservation in Sequence Logos implies DNA Distortion or Base Flipping during
Replication and Transcription Initiation for more information.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Globins
The end of the B helix through the beginning of the D helix of 34 globins.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Prenyltransferases (motif A)
Here is an alignment found by the gibbs sampling system. Both
the identified site and some context are shown. Note that
spaces are significant, so that the spaces included below (to aid
identification of the site) will end up being considered amino
acid positions.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
HTH Proteins
Helix-Turn-Helix DNA binding motifs found by the gibbs
sampling system. Compared to the CAP HTH logo there is
much less sequence conservation within the DNA binding
helix (11-17), as might be expected for a diverse sample of
proteins.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Human Splice Sites
These logos show a small sample of Human intron-exon splice boundaries.
Sequences of experimentally confirmed genes were extracted from EID: the
Exon-Intron database. Additional discussion of the features in this logo can
be found in the paper Features of spliceosome evolution...
- Exon-Intron (Donor) Sites
- Edit Logo Intron-Exon (Acceptor) Sites
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Practical
'to try in your own time”
• Interpret the conserved amino acids in your
alignments using logos
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Interpret the conserved amino acids in your alignments (e.g HSF1) using logos
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
