How to load biological sequences such as proteins, RNA and DNA using Jalview is demonstrated in this tutorial.
The video explains the different way to read sequences and sequence alignments into Jalview ( http://www.jalview.org). This is done by reading files saved in sequence alignment format, using ‘drag and drop’ and ‘cut and paste’ methods, using urls or linking to public databases.
In this video, the PFAM seed database id used is PF03460.
The Uniprot database ids are P00340 and P02144; P02185; P68082; P02189; P02210; P68082; P02190; P02205; P02197; P68276; P02186; P14396. The url of sequence I use in this video is http://www.jalview.org/tutorial/align....
Jalview software that can be downloaded onto your computer or run in a web browser. For more information please visit the Jalview website at http://www.jalview.org.
Jalview is a free, multiple sequence alignment visualisation software for editing, annotating and analysing proteins, RNA and DNA data. It is used to interactive investigate the primary, secondary and tertiary structure. Figures at journal publication standard can be generated from the results.
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. 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 analysis tools including (i) multiple sequence alignment, (ii) phylogenetic tree calculations and principal 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 has 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.
Loading protein sequences and alignments into Jalview protein structure and function ppt | |
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