The Jalview Resource for Biological Sequence, Structure and Function Analysis: 2019 and Beyond

The Jalview Resource is an open-source, GPL-licenced, graphical multiple sequence alignment editor and analysis workbench, first developed in 1996.

It is installed on >57,000 computers in >130 countries and publications describing Jalview have been cited >5,600 times.

In addition to sophisticated colouring, filtering, searching, alignment editing and annotation functions for DNA, RNA and Protein sequences, Jalview provides linked views of trees, three-dimensional structures and RNA secondary structure.

Eight standard multiple alignment algorithms, four disorder predictors, seventeen conservation methods, the JPred protein secondary structure predictor and RNAalifold RNA structure predictor are freely available in Jalview.

Users can interactively search PDBe and Uniprot, and retrieve alignments and genomic data from the Interpro and Ensembl data resources at the EMBL-EBI.

Wellcome Trust investment since 2014 enabled improvements, including efficient handling of long genes with large numbers of annotations, a linked DNA/RNA/protein multiple alignment window, discovering and displaying genetic variation from Ensembl, extended querying against PDBe and Uniprot EMBL-EBI services and the development of >30 training videos that have received >50,000 views.

Here we request support to extend the Jalview Resource to add sophisticated facilities for long RNA-read interpretation, reproducible data analysis, further links with EMBL-EBI, and a new web-friendly JavaScript version: JalviewJS.