How to locate Jalview's drop-down and context menus is demonstrated in this tutorial (http://www.jalview.org). It is part of the ‘Getting Started’ playlist.
The Jalview Desktop window and each of the sub menus have their own unique set of menus. They are easy to locate in the top left-hand corner of the window. Jalview also has a number of context menus that are not immediately visible, they are opened by positioning the mouse cursor in the appropriate region on the screen
and clicking the right mouse button.
Jalview is a free protein and nucleic acid sequence alignment visualisation software, with easy-to-use editing, annotation and analysis functionality. Sequences, alignment and additional annotation can be accessed from public databases. Journal quality figures can be generated from the results.
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.
Jalview can access wide range of data bases including PFAM, PDB, EMBL and Uniprot. It can read variety of file formats including FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm. It utilizes many different multiple sequence analysis tools such as Clustal, Muscle, MAFFT, Probcons, TCoffee.
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.
