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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  

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 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.