On Thursday 12th April 2018, as part of Alssundgymnasiet Sønderborg School visit to the School of Life Sciences.
There is a wealth of biological data deposited in free, publicly accessible databases. However, the bioinformatics information is frequently located in several databases and often have their own specific file formats. To assist research scientist, a team at the University of Dundee have developed a fully integrated, multiple window desktop called Jalview to visualize and analyses sequences and three-dimensional structures of proteins, RNA and DNA. For example, Jalview can access public biological databases, perform multiple sequence alignments, construct trees, predict protein secondary structure, annotate sequences and overlay features such as active site residues.
The hands-on workshop goals:
- To open Jalview from the ‘Launch Jalview Desktop’ link on the Jalview website and navigate the Jalview interface
- Fetch DNA and RNA sequences from public biological databases and colour the sequence bases
- Fetch myoglobin protein sequence from the UniProt database, colour the amino acid residues and view the 3D shape of the myoglobin
- View the myoglobin protein and the coding DNA (cDNA) in a split-screen window and identify the myoglobin exons
- Align the sequences using multiple alignment programs and generate a tree from the sequences
DNA ID: adz17331
RNA ID: 2gis
Protein ID: p02144
3D protein ID: 3rgk
Alignment url: http://www.jalview.org/tutorial/myoglobins.mfa
UniProt ID: P02144; P02147; P02185; P02192; P04247; P68276; P02197; P85077; P63113; P02190; P02187
Try this link: jnlp://www.jalview.org/webstart/jalview.jnlp or select and copy the text below into the clip board, and paste it into the Windows start menu, then press return ! (Press the windows button to open the start menu).
Remember to make sure the checkbox for 'Trust this publisher' is UNTICKED ! (this is a problem with our system here in Dundee).