How to colour sequence residues and alignments using Jalview is demonstrated in this tutorial (http://www.jalview.org). It is part of the ‘Colour, Appearance and Figure Generation’ playlist that explains how journal quality figures for publication can be generated.
Jalview has number of different colouring schemes available, they are either static or dynamic. The dynamic methods uses data such as conservation and consensus to control shading. How to customise colour schemes and threshold colour schemes based on annotations is demonstrated.
The PFAM seed database id used in the video is PF03460.
Jalview is free bioinformatics software for the multiple sequence alignment and structural analysis. It allows editing, annotating, analysing and visualisation proteins, RNA and DNA sequences.
Jalview has number of analysis tools to investigate protein structure and function including: (i) multiple sequence alignment, (ii) tree calculations and principle component analysis; (iii) consensus, conservation, and functional site analysis; (iv) secondary structure and disorder predictions; (v) visualisation of 3D structure.
This exercise can be found in our User Manual, available to download from the Jalview website (http://www.jalview.org/about/document...). Other Jalview training videos can be viewed at in the training section of the web site (http://www.jalview.org/training/Train...).
Jalview was developed in Geoff Barton's group (http://www.compbio.dundee.ac.uk) in School of Life Sciences (http://www.lifesci.dundee.ac.uk) at the University of Dundee (http://www.dundee.ac.uk) with the support of the BBSRC and Wellcome Trust. The team have also developed software JPRED (http://www.compbio.dundee.ac.uk/www-j...) and JABAWS (http://www.compbio.dundee.ac.uk/jabaws).
Jalview Online Training YouTube Channel is a free bioinformatics educational course suitable for Undergraduate and PhD students. Playlists include (a) Getting Started; (b) Selecting and Editing Sequences; (c) Colour, Appearance and Figure Generation; (d) Jalview Dundee. This online educational material was produced by Dr Suzanne Duce, School of Life Sciences, University of Dundee.
