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NEW! Resources for the Jalview Schools Workbook

'Visualising DNA, RNA & Proteins' Jalview Schools Workbook is aimed at 16-18 year old secondary school students studying 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 HBB gene, which is involved in sickle cell anaemia. The genetic mutations linked to this disease is identified by viewing the coding DNA and its protein product in a split-screen viewer.

Click to view the Schools Workbook pdf
View Sequences and 3D structures in JalviewJS

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 (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 Jalview JS
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

Jalview Videos

 

 

Click to view the video: Jalview- free software for multiple sequence alignment and analysis
Click to view the video: Navigating the Jalview desktop
Click to view the video: Jalview's multiple windows
Click to view the video: Jalview's drop-down and context menus

PDB IDs used in Project 1 & 2

PDB ID Molecule Function Link
3DSE DNA fragment  

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

2GIS RNA  

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

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

6bcx Insulin Signalling

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

1mbn 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)

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/).