Analysis of S-protein polymorphism

Live Resources

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What's the point?

In the previous portion of this study we found a non-synonymous polymorphism within the S-gene. In this section we are trying to interpret its possible effect.

Outline

Obtain coding sequences of S proteins from a diverse group of coronaviruses. Generate amino acid alignment to assess conservation of the polymorphic location.

Input

Downloaded CDS sequences of coronavirus Spike proteins from NCBI Viral Resource for the following coronaviruses:

These viruses were chosen based on a publication by Duquerroy et al. (2005). The sequences were extracted manually--a painful process. We will develop a tool for parsing particular CDS sequences automatically for future analyses.

Output

We produce two alignments, one at the nucleotide and one at the amino acid level, of Betacoronavirus spike proteins. The alignments can be visualized with the Multiple Sequence Alignment visualization in Galaxy :

Alignments of Spike proteins
A. CDS alignments
B. Protein alignment

Workflow and history

The Galaxy history containing the latest analysis can be found here. The publicly accessible workflow can be downloaded and installed on any Galaxy instance. It contains all information about tool versions and parameters used in this analysis.

The transeq tool converts the CDS sequences into protein sequences, which we then align to each other using mafft. The output is fed into tranalign along with the nucleotide sequences. tranalign produces a nucleotide alignment coherent with the protein alignment.

BioConda

Tools used in this analysis are also available from BioConda:

Name	Link
mafft
emboss