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.


Getting Started

(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.

Click to view the Getting Started using Jalview videos.
Click to view all the Jalview training videos.
These videos are located on the Jalview Online Training YouTube channel.


(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

PDB ID Molecule Function Link
3BSE DNA fragment  

http://pdb101.rcsb.org/motm/23

2GIS RNA  

http://pdb101.rcsb.org/motm/15

3nmm Haemoglobon Transport

http://pdb101.rcsb.org/motm/41

1smd Amylase Enzyme

http://pdb101.rcsb.org/motm/74

1cag Collagen Structure

http://pdb101.rcsb.org/motm/4

1igt Antibody Defence

http://pdb101.rcsb.org/motm/21

5xb1 Ferritin Storage

http://pdb101.rcsb.org/motm/35

6trz Insulin Signalling

http://pdb101.rcsb.org/motm/14

3rgk Myoglobin Transport

http://pdb101.rcsb.org/motm/1

Uniprot Myoglobin IDs used in Project 3

Uniprot ID

Species

P02144 Human
P02147 Gorilla
P02185 Whale
P02192 Cow
P04247 Mouse
P68276 Dolphin
P02197 Chicken
P63113 Dog
P02190 Sheep
P02187 Elephant

P02144; P02147; P02185; P02192; P04247; P68276; P02197; P85077; P63113; P02190; P02187

DNA Identifier Codes used in project 3 & 4

CAG46747 EmblCDS ID for MB gene that codes for myoglobin protein (P02144)
CAG46711 EmblCDS ID for HBB gene that codes for Hemoglobin subunit beta protein (P68871)

Other links

https://www.jalview.org/jalview-js/JalviewJS_noconsole.shtml?-props%20https://www.jalview.org/tutorial/schools/school.jalview.properties%20open%20https://www.jalview.org/tutorial/schools/1ribbon.jvp
https://www.jalview.org/jalview-js/JalviewJS_noconsole.shtml?-props%20https://www.jalview.org/tutorial/schools/school.jalview.properties%20open%20https://www.jalview.org/tutorial/schools/2StickBall.jvp
https://www.jalview.org/jalview-js/JalviewJS_noconsole.shtml?-props%20https://www.jalview.org/tutorial/schools/school.jalview.properties%20open%20https://www.jalview.org/tutorial/schools/3spacefill.jvp

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/)

Other Resources

Blackboard Collaborate Workshop Instructions

 


(F) Acknowledgements

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.