Principal components analysis of protein and nucleotide alignments in Jalview
Channel: Jalview & Dundee Resource Online Training
Date: 2020-03-13

Jalview is a free-to-use sequence alignment and analysis visualisation software linking genomic variants in DNA, protein alignments and 3D structure (http://www.jalview.org/). In this tutorial, we learn how to run principal components analysis in Jalview.

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.

The URL used in this video is http://www.jalview.org/tutorial/alignment.fa.

This exercise can be found in our User Manual, available to download from the Jalview website (http://www.jalview.org/about/documentation). Other Jalview training videos can be viewed in the training section of the website (http://www.jalview.org/training/Training-Videos).

Jalview can access a wide range of databases including PFAM, PDB, EMBL and UniProt. It can read a variety of file formats including FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm.
Jalview collaborates with several groups to offer a broad range of sequence analysis tools including: 
• multiple sequence alignment using Clustal Omega, Muscle, MAFFT, ProbCons, T-COFFEES, ClustalW, MSA Prob and GLProb
• tree calculations and principal component analysis (PCA)
• consensus, conservation, and functional site analysis
• secondary structure and disorder predictions
• visualisation of 3D structure.

Jalview (http://www.jalview.org/) has been developed in Geoff Barton's group (https://www.compbio.dundee.ac.uk/) in the School of Life Sciences (https://www.lifesci.dundee.ac.uk/) at the University of Dundee with the funding support of the BBSRC and the Wellcome Trust.

This video was produced by Dr Suzanne Duce, School of Life Sciences, University of Dundee.