Week 4 - Multiple Sequence Alignment

We now turn our attention to multiple sequence alignment (MSA); the alignment of 3 or more sequences. This is a computationally intensive task that has resulted in a very wide range of possible methodological solutions. This week we will learn about the methodologies used to create MSAs, breaking them up into several categories based on the approach used to solve the problem. We describe scoring strategies for MSAs remembering that MSAs are used to generate the BLOSUM and PAM matrices you have been using in pairwise sequence alignment and BLAST searching. We also look at some of the measures used to quantify/assess quality across an MSA.

Lecture 4 - Multiple Sequence Alignment

The lecture slides for Week 4 - "Multiple Sequence Alignment" are available here.

The video of the lecture will be available from the GitHub video area here.

Computing Labs

This week in the computing lab we will be working with some Python notebooks on BLAST and multiple sequence alignement. You can access all of the computing lab materials on our GitHub page.

There are challenges/tasks throught the notebooks for you to practice with. Please feel free to post in the Discussion board in the relevant section if you have any queries and/or comments.

Reading Lists & Resources

Each week we will have an accompanying reading list with some articles & web-sites for self study to support the course. You can find the course "Resource List" - here. We will continue to curate the list throughout the course especially if things pop up in the lectures and practicals that we want to add a reference or link to so do please check back in on the list from time to time.

We have generally tried to identify resources as "Essential", "Recommended" or "Further Reading" in an attempt to help you prioritise your reading during the course.

Finally a very important time to draw your attention to what you can consider the "core text" for the course, which is the excellent "Bioinformatics & Functional Genomics" Third Edition by Jonathan Pevsner. You will be pleased to know that this text-book is available free online as part of the University's subscription portfolio. You can find it right at the top of the resource list. If you have any problems accessing or using any of the above please do drop us a comment in the Discussion forum and we will try to get things resolved as soon as possible.

This week you should try to read Chapter 6 - "Multiple Sequence Alignment" of BFG.