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Building Multiple Sequence Alignments

The document outlines an online course module on Multiple Sequence Alignment, led by trainer Ahmed M. Alzohairy. It includes assignments focused on building alignments using various tools like ClustalW and MUSCLE, as well as tasks for sequence retrieval and analysis. Participants are instructed to upload their completed assignments to the Vula platform by specified deadlines.

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17 views2 pages

Building Multiple Sequence Alignments

The document outlines an online course module on Multiple Sequence Alignment, led by trainer Ahmed M. Alzohairy. It includes assignments focused on building alignments using various tools like ClustalW and MUSCLE, as well as tasks for sequence retrieval and analysis. Participants are instructed to upload their completed assignments to the Vula platform by specified deadlines.

Uploaded by

guitayaoba2
Copyright
© All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd

Introduction to Bioinformatics online course: IBT_2025

Module topic: Multiple Sequence Alignment


Contact session title: Building a Multiple Sequence Alignment
Trainer: Ahmed M. Alzohairy

Assignment – Building a Multiple Sequence Alignment

Introduction

Building multiple sequence alignments is far from an exact science. It’s


more art than science, requiring that you use everything you know in
bioinformatics and biology. The main idea behind building a multiple
sequence alignment is to put similar amino acids or nucleotides in the
same column if they contain the same criterion. There are four major
criteria most scientists use to build a multiple alignment of sequences
that all have different properties.

NB: Hand-in information - please upload your completed assignment to


the Vula ‘Assignments’ tab. Take note of the final hand-in date for each
assignment indicated on Vula

Tools used in this session

For building an MSA, the most popular programs. We will see the
differences between ClustalW, MUSCLE, and Tcoffee. And for analysis,
we will use other online tools.

Please note
 Hand-in information: Please upload your completed assignment
to the Vula assignments tab. Take note of the final hand-in date,
which will be indicated on Vula.
Task 1: Reading the slides
Task 1: instructions
Read and understand the contents of the PPT slides
Introduction to Bioinformatics online course: IBT_2025

Task 1: Sequence Retrieval and FASTA Formatting


Task:
Retrieve the HSF1 (Heat Shock Factor 1) protein sequence for Human,
Mouse, and Chicken from UniProt. Save them in a single file in FASTA
format.

Task 2: Aligning Sequences and Interpreting Conserved Regions


Task:
Align the retrieved sequences using Clustal Omega, then identify one
conserved block using the sequence logo from WebLogo.

Task 3: Extracting annotation (identifying conserved domain)


Task 3: instructions
Task 3: Memo answer MSA Software Matching Task: Match each MSA
tool to its optimal use case: COBALT, ClustalW, T-Coffee, MUSCLE,
MAFFT.
Best Use Case
- Domain-based alignment with constraints
- Widely used standard alignment method
- Small-size, highly accurate alignments
- Fast alignment for medium-sized datasets
- Fast and scalable for large datasets

Task 4: Fast alignment for medium-sized datasets


Task 4: List four biological applications of multiple sequence
alignments (MSA) and briefly explain their purpose.

Task 5: Troubleshooting a Poor MSA


Task 5: You attempted an MSA and obtained an alignment with many
gaps and low conservation. What steps can you take to improve it?

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