Making inferences from multiple sequence alignments of modular proteins

Renato Alves   2023-04-18   Comments Off on Making inferences from multiple sequence alignments of modular proteins

Date(s) - 2023-04-18
14:00 CEST - 17:00 CEST


Instructors / helpers

  • Toby Gibson
  • Manjeet Kumar
  • Jesús Alvarado Valverde
  • Renato Alves


This 3 hour afternoon course will be held in person.

"Nothing in Biology Makes Sense Except in the Light of Evolution" a phrase first coined by evolutionary biologist Theodosius Dobzhansky tries to highlight the importance of evolution when interpreting biological phenomena. Multiple sequence alignments (MSA) can provide such insights by enabling us to see the relationship between protein sequences of many different related organisms and their biological functions.

This course is aimed at illustrating useful points about protein sequence/structure/function relationships. Some sequence sets will be relevant to pathogen infection biology. For extra context, we may tap into tools other than sequence alignments such as Pfam, ELM, and UniProt. A web page will be prepared for the course and followed on the day. Participants will be able to use their own datasets during the course and are welcome to discuss their proteins with the trainer subsequently.


  • Basic concepts
  • Protein sequence analysis tools and databases
  • Alignment production and visualization through Jalview
  • Determination of structural features via MSA
  • Work on your own proteins


  • Protein sequence-structure-function relationship
  • Sequence homology
  • Types of multiple sequence alignments

Preparation in Advance

Preinstall and briefly test:

  • Clustal Omega for running MSA in the terminal (optional)
  • JalView for viewing sequence alignments and accessing remote alignment servers


EMBL Bio-IT and the Gibson Team will offer the course for free to all EMBL members.

The course is limited to 20 in-person (in Heidelberg) seats which shall be allocated on a first come first served basis.

Registration deadline: Friday, 14th April 2023 – 17:00


Bookings are closed for this event.

About Renato Alves

I am a Community and Project Manager for Bio-IT and Training Coordinator for ELIXIR Germany. Find me at EMBL-HD office 116 or at Bio-IT drop-in Sessions on Tuesdays 10:00-12:00 at the EMBL staff lounge (or online). Contact Details: email -, Twitter -, GitHub -, GitLab -, ORCID -