| usegalaxy.org | usegalaxy.eu |
|---|---|
 |
|
 |
|
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.
Obtain coding sequences of S proteins from a diverse group of coronaviruses. Generate amino acid alignment to assess conservation of the polymorphic location.
Downloaded CDS sequences of coronavirus Spike proteins from NCBI Viral Resource for the following coronaviruses:
| Accession | Descriptin |
|---|---|
| FJ588692.1 | Bat SARS Coronavirus Rs806/2006 |
| KR559017.1 | Bat SARS-like coronavirus BatCoV/BB9904/BGR/2008 |
| KC881007.1 | Bat SARS-like coronavirus WIV1 |
| KT357810.1 | MERS coronavirus isolate Riyadh_1175/KSA/2014 |
| KT357811.1 | MERS coronavirus isolate Riyadh_1337/KSA/2014 |
| KT357812.1 | MERS coronavirus isolate Riyadh_1340/KSA/2014 |
| KF811036.1 | MERS coronavirus strain Tunisia-Qatar_2013 |
| AB593383.1 | Murine hepatitis virus |
| AF190406.1 | Murine hepatitis virus strain TY |
| AY687355.1 | SARS coronavirus A013 |
| AY687356.1 | SARS coronavirus A021 |
| AY687361.1 | SARS coronavirus B029 |
| AY687365.1 | SARS coronavirus C013 |
| AY687368.1 | SARS coronavirus C018 |
| AY648300.1 | SARS coronavirus HHS-2004 |
| DQ412594.1 | SARS coronavirus isolate CUHKtc10NP |
| DQ412596.1 | SARS coronavirus isolate CUHKtc14NP |
| DQ412609.1 | SARS coronavirus isolate CUHKtc32NP |
| MN996528.1 | nCov-2019 |
| MN996527.1 | nCov-2019 |
| NC_045512.2 | nCov-2019 |
| NC_002306.3 | Feline infectious peritonitis virus |
| NC_028806.1 | Swine enteric coronavirus strain Italy/213306/2009 |
| NC_038861.1 | Transmissible gastroenteritis virus |
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.
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 |
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.
Tools used in this analysis are also available from BioConda:
| Name | Link |
|---|---|
mafft |
 |
emboss |
 |