Analysis of S-protein polymorphism
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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.
Obtain coding sequences of S proteins from a diverse group of coronaviruses. Generate amino acid alignment to assess conservation of the polymorphic location.
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
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
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.
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:
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Created: 25th Mar 2020 at 10:05
Last updated: 25th Mar 2020 at 11:23
Last used: 25th Sep 2022 at 15:59