Posts Tagged ‘alignment’

ABrowse alignment viewer for Pfam coronavirus families

April 24, 2020

The SARS-CoV-2 pandemic continues to stimulate a worldwide scientific response, with results and preprints accumulating at a high rate. In turn, these papers have generated extensive online discussion.

In order to help link these discussions to data, the protein domains in the Pfam SARS-CoV-2 special release are now available for browsing in ABrowse, a phylogenetic alignment and structure browser newly-developed by the team behind the JBrowse genome browser.

Using ABrowse, you can now link to dynamic views of individual domains from the special release. As an example of how this might be used, this is a link to the ORF7a protein, of which a 27 amino acid deletion was recently observed in Arizona. It can be seen quite clearly from the alignment that a 27aa deletion is a not-insignificant dent in this protein, suggesting (as hypothesized by Nick Loman) that this protein might not be necesary for efficient human-to-human transmission of SARS-CoV-2.

You can scroll around the alignment by dragging (ABrowse owes an inspiration debt to the BioJS MSA browser for this feature), and you can use the phylogenetic tree to the left of the alignment to collapse individual clades. ABrowse displays the collapsed clades as a sequence logo, using a probabilistic profile of the ancestral sequence (performed in a separate thread for performance reasons).

For sequences where Pfam includes a link to PDB structures, you can click on a hyperlinked sequence name to bring up a structure visualization using pv, the WebGL PDB viewer. Structures can be rotated, zoomed, or recolored. Mousing over alignment columns will highlight the corresponding residue in all open structures, and vice versa, allowing comparison of homologous amino acids in the structural context.

ABrowse

The image shows the Corona_S2 domain, i.e. the Spike glycoprotein, along with several structures and some ancestral sequence logos.

This version of ABrowse is an alpha release, and is likely to be updated; however, URL bookmarks use the Pfam accession numbers and the JBrowse/ABrowse team plans to keep the alignments up to date. If you have questions, bug reports, or feature requests about ABrowse, please feel free to post them to the ABrowse issues page and/or contact Ian Holmes.

Guest post by Ian Holmes