How to modifying the appearance of the Jalview alignment window is demonstrated in this tutorial (http://www.jalview.org). It is part of the ‘Colour, Appearance and Figure Generation’ playlist that explains how to produce journal quality figures for publication.
There are a number of ways to customise the Jalview alignment window for example the alignments can be displayed wrapped or unwrapped. Text font, style, size and colour can be changed. Plus there are a number of format menu options that can toggled on and off. The annotations visible and their order can be customised.
The sequence alignment url used in the video is http://www.jalview.org/tutorial.align...
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.
