Ancestry of MERS-CoV strains from camel host

[MManee]

• main reference paper: https://www.nature.com/articles/srep18825.pdf
• we have to replicate selected figures in reference paper
• replication is essential to check the quality of our pipeline

TO DO

• [x] we have to replicate figure1 and figure 2 using 70 human strains from reference paper
  • accession numbers and sequences in fasta format are located here: https://github.com/kacst-bioinfo-lab/labwork/tree/master/data/shared/mers_cov
• [x] we have to replicate figure 3 and table 1 for putative recombination regions

[bioinfo2016]

To make phylogenetic tree, it's recommended to use BEAST package. To download BEAST go to [http://beast.community/installing].

After preparing complete genome of all viruses in a fasta format, you should do the following steps:

1- Make multiple sequence alignment using MAFFT software and then convert it to nexus format. To convert alignment file to nexus format go to " https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html".

2- Load nexus file to BEAUti software to generate XML file.

Settings used in BEAUTi: In this project I make the settings of BEAUTi as follows:

Tips section : This section enables you to specify collection dates of all viruses. Tick “Use tip dates” and then select “Guess Dates “. Select “Defined just by its order” and choose “last” option from the drop-down menu and then press OK.

Sites Section: Here you can select which substitution model you use with your dataset. Select HKY substitution Model and the rest option is default.

Clocks: select “Uncorrelated relaxed clock” as clock type and “lognormal” as relax distribution.

Trees: Tree prior used in this work is “Bayesian SkyGrid”.

MCMC: Length of chain is 50 million and the input of the rest parameters is 25000.

3- Once BEAST XML file generated, use BEAST to perform the analysis. BEAST creates two files : log file and tree file.

4- To analyse BEAST output, upload log file to Tracer tool.

5- TraceAnnotator takes the tree file generated by BEAST and write the summarized tree in a file you specify it.

6- To visualize the phylogenetic tree that created by TraceAnnotator, use FigTree tool to make it.

[bioinfo2016]

To install MAFFT software on the srver:

1- Transfer the source package of MAFFT to a directory on the server. You can download the source package from: https://mafft.cbrc.jp/alignment/software/installation_without_root.html.

2- Then unzip the package using the following command:

tar xvf mafft-7.402-without-extensions-src.tar.

3- Edit the first line of Makefile in the 'core' directory as follows:

cd mafft-x.xxx-with-extensions/core/

vi Makefile (any other text editor is ok.) From: PREFIX = /usr/local To: PREFIX = /home/your_home/somewhere (must be absolute path). For example:/home/shomrani/maff-dir

4- Also edit the third line of Makefile From: BINDIR = $(PREFIX)/bin To: BINDIR = /home/your_home/bin.

5- Compile and install. % make clean % make % make install

Note: you do not need root permission.

[atalgarni]

https://www.nature.com/articles/emi201789#materials-and-methods

[bioinfo2016]

The attached file contains detailed info about experiments have been run by BEAST.

BEAST log file.pdf