Introduction to Bioinformatics
Online Course: IBT
Multiple Sequence Alignment
Building Multiple Sequence Alignment
Lec4: Coloring MSA for Publication
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Preparing Your Multiple Alignment for Publication
- You want to show this alignment to your
colleagues, you want to include it in publications
- In short, you need a high-impact picture to
convince people that your research is going well.
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
Introducing the Multiple Sequence Alignment Viewer (MSAV)
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
The MSA Viewer
<ncbi>/tools/msaviewer/
• A general purpose alignment viewer
• Useful for assessing sequence conservation,
sequencing errors or variations
• Flexible options for coloring alignments
• Plugs into NCBI alignment tools (BLAST, COBALT)
• Also accepts custom alignment data
• Easily embedded in your own web pages
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Display Feature: Annotations
(+) to see annotated:
Domains
Binding sites
Motifs
Other features
Requires NCBI accessioned sequences
5 Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Display Feature: Colors
Tools Menu
Colors emphasize
amino acid properties
conservation
column average
compared to Master
6 Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Display Feature: Residue Context
Click amino acid
position in sequence
position in alignment
sequence statistics
column statistics
7 Introduction to Bioinformatics Online Course:IBT
02/22/2017 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
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
Using Boxshade
Boxshade is a utility that allows you to put some life into your
alignment. It shades columns according to their level of
conservation and produces files that you can easily
manipulate for inclusion in reports or articles.
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
When pasting MSF or ClustalW files, please make sure
that the pasted text starts with the header line of the alignment and contains no extra blank
lines at the bottom.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Generates a file that most word processors
(such as Microsoft Word) can read
If your alignment is long, select a small font size.
consensus sequence that contains the most
common amino acid for each column.
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
If you request 0.5, for example, it means
you want half the residues to be
conserved for some shading to occur.
Select the format of the
multiple sequence alignment
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
Conservation doesn’t necessarily mean identity in Boxshade. Similar
residues, such as isoleucine and valine, also account for conservation.
Two types of shading exist:
• Black: Identical amino acids or nucleotides
• Gray: Similar amino acids
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
MView for colorful MSA
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
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Practical
(to try in your own time)
1. Point your browser to
www.ch.embnet.org/software/BOX_form.html.
2. Choose RTF_new from the Output Format drop-down menu.
3. Select the font size you want.
4. Choose Add a Consensus Line with Letters from the Consensus Line drop-down menu.
5. Select the fraction of sequences you would like shaded.
6. Select the format of the multiple sequence alignment you want to use.
7. Paste your multiple sequence alignment into the Sequence window.
8. Click the Run Boxshade button.
9. Click the here is your output link, save to a local file, then open the local file with Word.
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
