Learn Bioinformatics

Basic bioinformatics skills

This web portal hosts protocols with case studies on how to use web servers to solve bioinformatics problems. Teaching basic bioinformatics skills to students is based on these protocols which contain detailed descriptions of how to apply a bioinformatics tool to a problem.

The protocols were written by the Research Unit in Bioinformatics (RUBi) MSc and PhD students, based on a template that the director (Professor Ozlem Tastan Bishop) of the group prepared. Thirteen (13) such protocols were written, and students need to demonstrate the use of four of the protocols in their projects. All the protocols used web servers for the calculations, so avoiding the issue of getting specialized software installed in University computer labs.

Below are the different protocols:

  • NCBI-BLAST
  • Multiple Sequence Alignment
  • Protein Data Bank
  • Visualization Programs
  • HHpred
  • PRIMO
  • Protein-ligand Interaction
  • Protein Motif Analysis with MEME suite tools
  • Physicochemical Properties
  • Protein Interaction Calculator (PIC)
  • Alanine Scanning
  • Single Nucleotide Polymorphism (SNP) effect prediction
  • Using I-TASSER

Students are encouraged to follow these protocols after attending the lectures to get familiar with bioinformatics related topics. The purpose of these protocols is to guide the students while doing their projects. The aim is to provide a broad overview of the subject without entering any depth. Examples are given when teaching about the different bioinformatics topics. Peer learning is used when teaching the students for them to work in one of the projects.