Introduction to Bioinformatics

Online Course: IBT

Multiple Sequence Alignment
Building Multiple Sequence Alignment
Lec2 Choosing the Right Sequences

Introduction to Bioinformatics Online Course:IBT

Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
 Choosing the Right Sequences
“Before you build your alignment, you must carefully
select the sequences you want to align. These sequences
are members of the same protein family, and they all
share a common ancestor. The family is usually too large
to be entirely included in your multiple alignment, and
picking the right sequences is an art.”

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
Retrieve Sequences from Uniprot (www.uniprot.org

Introduction to Bioinformatics Online Course:IBT

Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Retrieve Sequences from NCBI (https://www.ncbi.nlm.nih.gov/protein)

Introduction to Bioinformatics Online Course:IBT

Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
 A Few Guidelines for Selecting Sequences
Proteins or DNA
Use proteins whenever possible. You can turn them back
into DNA after doing the multiple alignment.
If the sequences are non-coding sequences, you must use
DNA

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
 A Few Guidelines for Selecting Sequences
Many sequences

Start with 10–15 sequences; avoid aligning more than 50

sequences.

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
 A Few Guidelines for Selecting Sequences

Very different sequences

Sequences that are less than 30 percent identical to more

than half the other sequences in the set often cause troubles.

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
 A Few Guidelines for Selecting Sequences

Identical sequences
They never help. Unless you have a very good reason to do
so, avoid incorporating into your multiple alignment any
sequence that’s more than 90 percent identical to another
sequence in the set.

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
 A Few Guidelines for Selecting Sequences

Partial sequences
Multiple-sequence-alignment programs prefer sequences that are
roughly the same length. Programs often have difficulties comparing
items in a mixture of complete sequences and shorter fragments.

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
 A Few Guidelines for Selecting Sequences
Repeated domains
Sequences with repeated domains cause trouble for most multiple-alignment
programs — especially if the number of domains is different. When this happens,
you may be better off extracting the domains yourself with Dotlet or Lalign and
making a multiple alignment of those segments.

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
 A Few Guidelines for Selecting Sequences

If you still cannot generate a proper alignment from

sequences that you know are related, you could use a local
multiple alignment method, such as the Gibbs sampler, or a
pattern extraction motif, such as Pratt.

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
Paste your sequences here

Introduction to Bioinformatics Online Course:IBT

Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
 For carrying out a phylogenetic analysis on a set of coding DNA sequences,
do the following:

1. Translate your DNA sequences into proteins.

2. Perform the multiple alignments on the proteins.

3. Thread the DNA back onto the protein multiple sequence alignment
framework using pal2nal (coot.embl.de/pal2nal) or Protogene if you do
not have the original DNA sequence (www.tcoffee.org).

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
Paste your sequences here

Introduction to Bioinformatics Online Course:IBT

Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
 Choosing the right number of sequences
1- you should start with a relatively small number of sequences —
between 10 and 15 sequences would be suitable for most cases.

2- After you get something interesting happening with this small set, you can
always increase its size.

3- it’s hard to see any reason for generating a multiple alignment with more than
50 sequences, unless you’re interested in building some extensive phylogenetic
tree.

Introduction to Bioinformatics Online Course:IBT

Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
 Why you should not use too much sequences to align?
1- Computing big alignments is difficult.
2- Building big alignments is difficult
3- Displaying big alignments is difficult.
4-Using big alignments is difficult.
5-Making accurate big alignments is difficult

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
 Should you choose sequences that are very similar or
very different?
- Make the right compromise between similarity and
new information
- An alignment that only contains very similar
sequences brings little information.
- You can use it to extrapolate annotations, but you
can’t do phylogeny, structure prediction, function
perdiction, or any of the other useful applications
that we mentioned before

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
The general rule is that you
want them to be as distantly
related as possible - without
requiring too many gaps in
order to be properly aligned.
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
 Two things multiple-sequence-alignment programs really don’t like are

1- Sequences that are very different from every other

sequence in the group
2- Sequences that need long insertions/deletions to
be properly aligned

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
 Gathering your sequences with online BLAST servers

Characterized sequences: Try to include sequences with good

annotations and experimental information in your alignment
because they bring biological information with them — and also
allow feature propagation.

Uncharacterized sequences: including them in your multiple

alignment is to distinguish between the conserved positions that
cannot mutate and the other, less-important columns. They help in
getting some contrast on your sequence of interest.

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
Sequences that are so similar to the
query are probably homologous.
We commonly refer to such
sequences as hits or matches.

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
 Choosing the Right Method of Multiple Sequence Alignment
ClustalOmega
The most commonly used multiple sequence alignment package. Clustal Omega
is a new multiple sequence alignment program that uses seeded guide trees and
HMM profile-profile techniques to generate alignments between three or
more sequences

Paste your sequences here

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
 Choosing the Right Method of Multiple Sequence Alignment

2-Tcoffee
One of the latest multiple-sequence-alignment packages that you can use. With Tcoffee,
you can combine sequences and structures, evaluate an alignment, or merge
several alternative multiple alignments into a single unified result.

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
 Choosing the Right Method of Multiple Sequence Alignment
Continue……..

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
 Choosing the Right Method of Multiple Sequence Alignment

3- MUSCLE
One of the fastest alignment methods around for aligning large set of sequences

Paste your sequences here

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
 4- COBALT
Constraint-based Multiple Alignment Tool

Paste your sequences here

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