Jalview is a free protein, RNA and DNA sequence visualisation software. In this tutorial, how to use principal components analysis of alignments in Jalview is demonstrated (http://www.jalview.org).
The URL used in this video is http://www.jalview.org/tutorial/align...
Principal Components Analysis is an alternative to cluster analysis as a way to visualise groups of similar sequences. Similar sequences lie close to each other in 3D space. By default, the protein principal components analysis uses BLOSUM 62 pairwise substitution scores. The calculation method can be modified by going to the ‘Change Parameters’ drop down menu. PCA can also be performed on nucleotide alignments.
Jalview collaborates with several groups to offer a broad range of sequence analysis tools 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 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). The team have also developed software JPRED (http://www.compbio.dundee.ac.uk/www-j...) and JABAWS (http://www.compbio.dundee.ac.uk/jabaws).
Video production by Dr Suzanne Duce, School of Life Sciences, University of Dundee
