Visualising DNA, RNA & Proteins Jalview School Workbook Resources
Visualising DNA, RNA and proteins workbook is aimed at 16-18 year old secondary school students studying Higher, Advanced Higher or A level biology.
The easy-to-use design requires only a desktop or laptop computer with a web browser and internet access.
The workbook contains 4 practical web-based bioinformatic projects:
Project 1 views DNA and RNA sequences and their 3D structures.
Project 2 views protein sequences and their 3D structures.
Project 3 compares the sequence of human myoglobin protein with myoglobin sequences from other animals; then the student views the coding DNA sequence, and codons, alongside the protein.
Project 4 views exons and introns in the human haemoglobin subunit beta (HBB) gene. This is the gene involved in sickle cell anaemia, an inherited red blood cell disorder which affects millions of people throughout the world. The genetic mutations linked to this disease is identified by viewing the coding DNA and its protein product in a split-screen viewer.
Getting started:
(i) Click on the ‘View the School Workbook’ link in Section 1 to open the booklet in an adjacent window, or download the pdf depending on the browser.
(ii) Follow the instructions in the workbook, the links in Section 2 start each exercise by launching JalviewJS and loading the sequences.
If you get stuck, the videos in section (b) may help.
(1) Click to View the School Workbook in an adjacent web browser tab
(2) Follow the Instructions in the School Workbook
Use the links below to open JalviewJS in the web browser and view the molecules.
Note it may take a few seconds to open JalviewJS and load the sequences.
Project 1-Exercise 1: Click to View DNA fragment (3BSE) in JalviewJS
Project 1-Exercise 2: Click to View RNA (2GIS) in JalviewJS
Project 2-Exercise 1: Click to View Myoglobin protein (1mbn - transport) in JalviewJS
Project 2-Exercise 1: Click to View Collagen protein (1cag - structure) in JalviewJS
Project 2-Exercise 1: Click to View Amylase protein (1smd - enzyme) in JalviewJS
Project 2-Exercise 1: Click to View Antibody protein (1igt - storage) in JalviewJS
Project 2-Exercise 1: Click to View Insulin protein (6bcx - signalling) in JalviewJS
Project 2-Exercise 1: Click to View Ferritin protein (5xb1 - storage) in JalviewJS
Project 3-Exercise 1: Click to View Myoglobin Sequences and create a Tree in JalviewJS
Project 3-Exercise 2: Click to View Myoglobin protein & its coding DNA in JalviewJS by reading in file CAG46747 from EMBLCDS database
Project 4-Exercise 1: Click to View Exons & Introns in the HBB gene in JalviewJS
Project 4-Exercise 2: Click to View the coding DNA & its protein product in JalviewJS by reading in file CAG46711 from EMBLCDS database
(3) Frequently Asked Questions
I am having trouble viewing the 3D structure in Project 2?
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).
(A) School Workbook Videos
School Video 1: Bioinformatics and Big Data - 1 min 45 sec background video that considers why we need bioinformatics software such as Jalview
School Video 2: Introducing Jalview School Workbook - 2 min introduction video about Jalview and the 4 school workbook projects
School Video 3: HELP running the Jalview School Workbook Projects - 5 min FAQ video provides background information to get up and running
(B) Read 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) Database Identifiers and Links
PDB IDs used in Project 1 & 2
| PDB ID | Molecule | Function | Link |
|---|---|---|---|
| 3DSE | DNA fragment | ||
| 2GIS | RNA | ||
| 1smd | Amylase | Enzyme | |
| 1cag | Collagen | Structure | |
| 1igt | Antibody | Defence | |
| 5xb1 | Ferritin | Storage | |
| 6bcx | Insulin | Signalling | |
| 1mbn | Myoglobin | Transport |
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/).
(E) Other Resources
Project 1 Walkthrough Video
;
Project 3 & 4 Walkthrough Video
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.