Visualising DNA, RNA & Proteins Jalview School Workbook Resources
We have 4 easy-to-run web-based bioinformatic projects aimed at 16-18 year old secondary school students studying Higher, Advanced Higher or A level biology.
Project 1: single click exercise to view DNA & RNA sequences and their 3D structures.
Project 2: single click exercise to view human myoglobin protein sequence and 3D structure, then compares the sequence, using a similarity tree, with myoglobins from other animals.
Project 3: single click exercise to view the sequences and 3D structure of proteins with a range of different functions.
Project 4: exercise to view the exons and introns in the HBB gene and identify the genetic mutation in the DNA that is linked to sickle cell anaemia and view its location on the haemoglobin protein.
Requirement: Computer with a web browser and internet access.
(1) Click to open the School Workbook in an adjacent window (or download depending on the browser)
Recent update: 5th May 2021
(2) Follow the instructions in the School Workbook
Use the links below to run each exercise by launching JalviewJS in the web browser. It may take a few seconds to load the sequences.
Project 1-Exercise 1: Click to View DNA fragment in an adjacent browser
Project 1-Exercise 2: Click to View coding sequence of DNA and codons alongside the protein product in an adjacent browser
Project 1-Exercise 3: Click to View RNA in an adjacent browser
Project 2-Exercise 4: Click to View human myoglobin protein
Project 2-Exercise 5: Click to View myoglobin from different species and create a Tree
Project 3-Exercise 6: Click to View Haemoglobin protein (transport)
Project 2-Exercise 1: Click to View Collagen protein (structure)
Project 2-Exercise 1: Click to View Amylase protein (enzyme)
Project 2-Exercise 1: Click to View Antibody protein (defence)
Project 2-Exercise 1: Click to View Insulin protein (signalling)
Project 2-Exercise 1: Click to View Ferritin protein (storage)
Project 2-Exercise 1: Click to View Myoglobin protein (transport)
Project 4-Exercise 7: Click to View Exons & Introns
Project 4-Exercise 8: Click to View the coding DNA & its protein product
Project 4-Exercise 8 ADVANCED VERSION: click to View the coding DNA & its protein product from original databases with CAG46711 from EMBLCDS database
Jalview School Videos
Bioinformatics and Big Data - considers why we need bioinformatics software such as Jalview
Introducing Jalview School Workbook - about the Jalview school workbook projects
The RCSB PDB Newsletter article about the Jalview School Workbook
(C) What is Jalview?
Jalview is one of the most widely used applications for visualising and analysing DNA, RNA and protein multiple sequence alignments. It is free-to-use computer software with an interactive multi-window interface. This allows researchers to read files directly from public biological databases and view sequences, 3D structures and evolutionary trees. Jalview has a number of analysis tools for aligning sequences, measuring similarities, exploring features and comparing structures. Jalview has been developed in Prof Geoff Barton's group in School of Life Sciences the University of Dundee, with the funding support of the BBSRC and the Wellcome Trust.
(D) Frequently Asked Questions
I am having trouble viewing the 3D structure in Project 3?
Loading the 3D structure requires opening a context menu, with context menus the position of the mouse is significant. Place the mouse over the names of the sequences and then right click the mouse, and the required context menu should menu appears.
This manoeuvre is demonstrated in the Jalview School Video 3 (https://youtu.be/AIcpe7bzVdc?t=65).
(E) Database Identifiers and Links
PDB IDs used in Project 1 & 2
Uniprot Myoglobin IDs used in Project 3
P02144; P02147; P02185; P02192; P04247; P68276; P02197; P85077; P63113; P02190; P02187
DNA Identifier Codes used in project 3 & 4
Free Public Biological Databases
(i) UniProt is a database of protein sequences (http://www.uniprot.org/).
(ii) Protein Data Bank (PDB) is a database of crystallographic, three-dimensional structural data of large biological molecules (http://www.rcsb.org/).
(iii) Ensembl is a genomic database (http://ensemblgenomes.org/).
(iv) EMBL (CDS) data originates from the European Nucleotide Archive (ENA) database of annotated DNA and RNA sequences (https://www.ebi.ac.uk/ena).
(v) PFAM is a database of protein families is a database of protein families (http://pfam.xfam.org/)
(vi) RFAM is a database containing information about non-coding RNA families and other structured RNA elements (https://rfam.xfam.org/)
Blackboard Collaborate Workshop Instructions
The workbook was produced by Suzanne Duce with help from Mungo Carstairs, Benedict Soares, Bob Hanson, Dmitry Finkelbergs, Charlotte Campbell, Jim Procter and Geoff Barton.