Introduction to Bioinformatics online course: IBT
Practical Assignment
Module name: Sequence alignment theory and applications
Session name: Pairwise Sequence Alignment
Trainer: Jonathan Kayondo, Sonal Henson
Participant: Abinet Tesfaye
Date: January 3,2026
Pairwise Sequence Alignment
Introduction
Sequence alignment is a complex biological task with several strategies and programs
to pick from. The methods usually require intelligent use of several variables in the
programs. Dynamic programming helps with finding optimal sequence alignments.
This exercise demonstrates the usefulness of the local alignment in bioinformatics,
and also what can go wrong if you are not careful in choosing your parameters. We
also look at the dynamic programming applications in the Needleman-Wunsch
algorithm.
Tools used in this session
Uniprot - [Link]
EMBOSS Water – [Link]/Tools/psa/emboss_water/
EMBOSS Needle - [Link]/Tools/psa/emboss_needle/
TeachEnG - [Link]
Please note
Hand-in information If you are formally enrolled in the IBT course, please
upload your completed assignment to the Vula ‘Assignments’ tab. Take note
of the final hand-in date for each assignment, which will be indicated on Vula.
Task 1: Local vs Global alignment and choosing the correct parameters.
Task 1: instructions
The local alignment finds regions of local similarity. It is implemented trough Smith–
Waterman (but other also) algorithm. It has many purposes, and just some of them
are finding motifs, finding one sequence within another, search sequence databases,
etc.
Introduction to Bioinformatics online course: IBT
Using the Smith-Waterman algorithm we will make a local pairwise alignment of an
unknown sequence to the ACV synthetase of Penicilliumchrysogenum and investigate
the effect of adjusting the alignment parameters on the output.
1. Go to [Link] and download the sequence for ACV synthetase of
Penicillium chrysogenum (accession number: P26046).
2. Download unknown_sequence.fasta from Vula -> Practical Assignments ->
Module 3 Session 2
3. Go to [Link]/Tools/psa/emboss_water/ to make your alignment.
4. Upload or paste the P. chrysogenum sequence in the first box and the
unknown sequence in the second box.
5. Click ‘Submit’ to execute the alignment.
6. Click on ‘View Alignment File’ and save your alignment output in a text file.
7. Go back to the alignment submission page and repeat step 4.
8. Click on ‘More options’ under Step 2 and set the Gap Open and Gap Extend to
minimum.
9. Submit your alignment.
10. How does your alignment from step 5 and step 9 compare in terms of
alignment score, % identity, % similarity, gaps, and the extent (positions) of
alignment of the two sequences?
11. Now use the Needleman-Wunsch algorithm for global pairwise alignment to
align the two sequences from steps 1 and 2. You can use the EBI tool Needle
for that ([Link]
12. Follow steps 4-6 to submit the alignment.
13. How does your alignment compare with that from step 6?
14. Repeat steps 8 and 9, this time on the Needle program.
15. How does the alignment compare to that from step 12 (using default
parameters)?
16. This exercise demonstrates the usefulness of the local alignment in
bioinformatics, and also what can go wrong if you are not careful in choosing
your parameters.
Task 1: participant’s answer
<start typing your answer here>
Task 2: Dynamic programming
Task 2: instructions
Introduction to Bioinformatics online course: IBT
1. Go to TeachEnG ([Link] and play the Sequence
Alignment game. Click on the ‘Play’ button on the right of the page. Try all
the three levels. Test the effect of adjusting the parameters on the overall
score.
2. Similarly, play the Needleman-Wunsch algorithm game. Fill out the dynamic
programming matrix. Refer to the Instructional Material for help on how to
play the game.
Task 2: participant’s answer
<start typing your answer here>