Viewing DNA, RNA & Proteins in Jalview School Resources
4 easy-to-run web-based bioinformatic projects that are aimed at 15-18 year old secondary school students who are studying biology at Higher, Advanced Higher or A level.
Project 1: single click exercise to view DNA & RNA sequences and 3D structures.
Project 2: single click exercise to view a human myoglobin protein sequence and its 3D structure, followed by an exercise that uses a similarity tree to compare the myoglobin sequences from different animals.
Project 3: single click exercises to view the sequences and 3D structures of proteins with a range of different biological functions.
Project 4: exercise to view the exons and introns in the HBB gene and identify the genetic mutation on DNA that is linked to sickle cell anaemia and view its location on the 3D structure of haemoglobin protein.
Requirement: Computer with a web browser and internet access. Since JalviewJS opens inside a web browser, no software has to be downloaded.
Open the Workbook
Click the link to view the Workbook in an adjacent window (or download depending on the browser).
Next follow the instructions for each exercise.
Links to Run the Exercises
Clicking the links below will launch JalviewJS in an adjacent web browser tab and open files as appropriate.
Note: It may take a few seconds to load the sequences.
Project 1-Exercise 1: Click to view DNA fragment
Project 1-Exercise 2: Click to view the coding sequence of DNA & codons alongside the protein product
Project 1-Exercise 3: Click to view an RNA molecule
Project 2-Exercise 4: Click to view Human Myoglobin protein sequence and 3D structure
Project 2-Exercise 5: Click to view Myoglobin protein sequences 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 in the DNA of the HBB gene
Project 4-Exercise 8: Click to view the coding DNA of the HBB gene & its protein product
Advanced Exercise 1: Click to open JalviewJS desktop window in an adjacent browser window
Advanced Exercise 2: Click to view the coding DNA of the HBB gene & its protein product - reading files from the public biological databases (EMBLCDS id CAG46711)
Jalview School Videos
(i) Bioinformatics & Big Data - considers why we need bioinformatics software such as Jalview
(ii) Introducing the Jalview School Workbook Projects
(iii) What is Jalview?
Jalview is one of the most widely used applications for visualising and analysing DNA, RNA and protein alignments. It is free-to-use computer software with an interactive multi-window interface. This allows scientists 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.
Frequently Asked Questions - I’m having trouble viewing the 3D structure
Loading the 3D structure requires opening a context menu. The position of the mouse is critical when opening context menus.
Place the mouse over the name of the sequences (not the sequences themselves).
Then right click the mouse to open the context menu. This manoeuvre is demonstrated in the Jalview School Video above.
The RCSB PDB Newsletter article featuring the Jalview School Workbook
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/)
Database Identifiers
PDB IDs used in the workbook
| PDB ID | Molecule | Function | Link |
|---|---|---|---|
| 3BSE | DNA fragment | ||
| 2GIS | RNA | ||
| 3nmm | Haemoglobon | Transport | |
| 1smd | Amylase | Enzyme | |
| 1cag | Collagen | Structure | |
| 1igt | Antibody | Defence | |
| 5xb1 | Ferritin | Storage | |
| 6trz | Insulin | Signalling | |
| 3rgk | Myoglobin | Transport |
Uniprot Myoglobin IDs used in the workbook
| 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
EmblCDs IDs used in the workbook
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)
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.