Making the most of your Multiple Sequence Alignments (MSAs)

Manual Refinement, Tools, Concepts, Applications

Aidan Budd and David Judge

Thursday 1st March - Friday 2nd March 2007

Jointly organised by:

Depatment of Genetics, Cambridge University

EMBL (European Molecular Biology Laboratory)

Target Audience

This course is aimed at wet-lab scientists who already have a basic level of bioinformatic user experience. This includes the ability to save, find, and open files, to execute local programmes, use web-browsers (ideally in a UNIX-like environment) - along with the obtaining and manipulating of biological data on a computer e.g. sequence and structure data. The aim is to build upon your initial set of skills, allowing you to improve your ability to carry out analyses that depend on the creation of multiple sequence alignments (this covers a wide range of different applications including phylogenetic analysis, secondary structure prediciton, sensitive sequence similarity searching, and homology modelling).

However, having said that, there will be several instructors on hand to provide help in gaining familiarity with the more basic bioinformatic user skills, so less experienced scientists. To additionally support the less-experienced computer users amongst the attendees, we would also ask you to work together, in pairs, where possible making sure one of you has at least this basic level of bioinformatic user experience (we also find that in general people learn more from these courses when they work together with others.)

"How To"'s

Follow the link below for hints on how to carry out certain standard tasks need during multiple sequence alignment related analyses

"How To"'s for multiple sequence alignment

Below is a short document describing the basic interactions you are likely to need while manipulating files during the course

Unix usage notes


Follow the link below to a file containing a list of the different pieces of software used throughout this course, along with links to the websites for the software

MSA-related software


(Subject to adjustment based on the time required to complete the different items)

Thursday 1st March

Morning Session (9.30 - 13.00)

Introduction - Presentation
What is an MSA? - Interpreting MSAs in an evolutionary context - Software used in generating MSAs - Generic MSA workflow

Introduction - Practical
Retrieving sequences for MSA with keyword searches using SRS and ENTREZ, sequence similarity searches using BLAST - Introduction to automatic alignment software and alignment visualisation software

Application of MSAs - Presentation
Focus on phylogenetic analysis and secondary structure prediction -Importance of selecting sequences appropriate for problem being addressed - Other applications

Afternoon Session (14.00 - 17.30)

Applications of MSA - Practical
Influence of alignment quality on analysis results

Note that throughout these exercises the following formating is used to specify different types of text

Bold non-italic text like this gives you instructions about tasks you should carry out e.g. "View the following webpage"

Italic text specifies questions for you to answer

Back to Gibson Team course pages at EMBL.