Introduction to Bioinformatics
Online Course: IBT
Multiple Sequence Alignment
Building Multiple Sequence Alignment
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
COBALT
Constraint-based Multiple Alignment Tool
COBALT computes a multiple protein sequence alignment
using conserved domain and local sequence similarity
information.
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
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
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
Clustal Omega
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
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
Lec3: Tcoffee and MUCLE in more details
Aligning sequences and structures with Tcoffee
More accurate alignments at the cost of a slightly longer running time
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
http://tcoffee.crg.cat/
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
Past your sequences here
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
RNA Alignment
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
Paste your sequences here
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Protein Alignment
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
Paste your sequences here
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
Paste your sequences here
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
Paste your sequences here
Paste your sequences here
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Evaluation
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
- Give TCOFFEE a multiple alignment that
you generated with your favorite
method, and you can ask Tcoffee to
evaluate the quality of this multiple
sequence alignment for you.
- You can use any of the most common
formats (MSF, ALN, FASTA, and PIR).
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
Paste your sequences here
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
Paste your sequences here
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Advanced
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
TCOFFEE results
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
Crunching large datasets with MUSCLE
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
MUSCLE is a newcomer in the multiple-
sequence-alignment arena — but it is a
remarkably efficient package for making
fast, high-quality multiple sequence
alignments. MUSCLE is ideal if you want
to align several hundred sequences.
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
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
2
1
3 4
Introduction to Bioinformatics Online Course:IBT
Multiple Sequence Alignment| Prof. Ahmed M. Alzohairy
Practical
'to try in your own time
1- For your set of HSF1 FASTA sequences, what are the right TCOFFEE flavor to align them?
2- For your set of HSF1 aligned sequences, use the right TCOFFEE flavor to evaluate your
alignment?
3- Calculate the timing for Aligning your sequence collection using MUSCUL, TCOFFEE and
Clustal Omega and order them based on their speed?
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
