Analysis of the genetic sequence of the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compared with other viruses from the same familly (Coronaviridae) in diferent hosts. We will use clustal Omega that use seeded guide trees and HMM profile-profile techniques to generate alignments between multiple sequence. From this alignement a distance matrix can be extracted and used to generate the phylogenetic tree.
IDs-Hosts
- MN908947 : H. Sapiens (Human SARS-CoV-2)
- NC_019843: H.Sapiens (SARS-CoV-1)
- MN996532: Rhinolophus affinis coronavirus (RaTG13)
- MT121216: Manis javanica (Pangolin) coronavirus
- JQ065048 Wigeon coronavirus
- NC_034972: Rodent coronavirus
The sequences data (fasta files) can be found in the online public library: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/
Next we explore different sequences of ACE2 (the cell receptor used by the virus) among different species:
Sequences from NCBI aligned to reference genome (NC_045512.2) Variant calling using samtools.
- Biopython
- clustral (for alignement) Note: alignement can also be performed directly on https://www.ncbi.nlm.nih.gov/labs/virus/vssi/ before downloading the sequences.
- BWA
- Samtools