Jalview is a free protein, RNA and DNA sequence visualisation software. In this tutorial, how to perform multiple sequence alignment (MSA) and analysis is demonstrated (http://www.jalview.org). It explains how individual regions in an alignment can be aligned independently.
The URL used in this video is http://www.jalview.org/tutorial/unali...
A wide range of different protein sequence alignment algorithms such as Clustal Omega, Muscle, MAFFT, ProbCons, T-COFFEES, ClustalW, MSA Prob and GLProb can be run from within Jalview. The multiple sequence alignment tools can be found in the ‘Web service’ drop down menu. Jalview provides default settings for the alignment services; pre-sets are available optimized for specific types of alignment tasks; also the MSA parameters can be customized.
Jalview has over 17 different amino acid conservation measures that can be applied to the alignment. These can be accessed by going to the Web Service menu selecting ‘Conservation’ option and ‘AACon Calculation’.
The sequence located at http://www.jalview.org/tutorial/unali... was used in the video. 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 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
