How to select residues, sequences and columns from sequence alignment using Jalview is demonstrated in this tutorial.
The different ways to select residues, sequences and columns in Jalview are demonstrated using the click-and-drag, the keyboard shortcuts and the cursor mode methods (http://www.jalview.org).
The PFAM seed database id used in the video is PF03460.
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 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.
Jalview collaborates with several groups to offer a broad range of sequence analysis tools including: (i) multiple sequence alignment, (ii) phylogenetic 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) 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.
