Loading protein sequences and alignments into Jalview
Channel: Jalview & Dundee Resource Online Training
Date: 2019-10-24

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/). This video explains how load biological sequences such as proteins, RNA and DNA by either 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 the sequence 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 collaborates with several groups to offer a broad range of sequence analysis tools including:
(i) multiple sequence alignment (MSA),
(ii) tree calculations and principal component analysis (PCA);
(iii) consensus, conservation, and functional site analysis;
(iv) secondary structure and disorder predictions;
(v) 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.