Tasks

Create a file for the report (<your_name>.docx).

1. GENOME
   1. Chose a virus and download its genome. Socially important viruses are preferable.
   2. Describe the genome: size, RNA or DNA, number of proteins encoded etc. Chose one protein for further work
2. COMPARE TWO GENOMES

   1. Choose genome of another virus from the same family or genus.

   2. Create dotplot of the two genomes and describe rearrangements.
   3. Is it correct that borders of the rearrangements are not inside genes?
3. FAMILY OF THE PROTEIN
   1. Choose a protein (viral one or any other)
   2. Find and download sequences of all homologous proteins within the certain taxon (Family? For example).
   3. Align the sequences and revise the alignment
   4. Reconstruct a phylogenetic tree.
4. 3D PROTEIN STRUCTURE
   1. Find homologous proteins in the PDB.

   2. Open the 3D stucture of one of found proteins using JSmol applet on its web page at the PDB site ( http://www.rcsb.org/ )

   3. Create and incude into your report a nice image (-s) demonstrating the protein and its contacts with a ligand (if any)
   4. Find about 10 sufficiently distant homologs of the protein whose 3D structure you have studied. Use Blast of this potein sequence. "Sufficiently distant homologs" means that the percent of identity between your protein and each homolog is between 30% and 60%. Align the sequences of your protein and of selected homologs.
   5. Select a conserved block in the alignment
   6. Describe the role of few conserved positions in the 3D structure
   7. (-) Create a 3D model of your protein based on homology to a protein with known 3D structure.
   8. (-) Superpose the model and the template
5. PROTEIN DOMAINS
   1. Describe the domain architecture of your protein
   2. Select one of domains of your protein and describe several domain architectures including this domain
6. Extra task. FIND and ANNOTATE ONE GENE in a CONTIG of the UNANNOTATED GENOME

   1. Choose any contig of an appropriate length (10 – 30 Kb) from the genome of Amoeboaphelidium protococcarum. File with the genome is "X5.fasta". File with the lengths of contigs is "X5.info".

   2. Predict genes by similarity with known proteins (using the appropriate version of BLAST against a protein database).
   3. For one found gene predict its function by homology.

Hints

4g Use https://swissmodel.expasy.org/ server

4h For superimposition of two or more 3D structures use any of two services

http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver

http://yanglab.nankai.edu.cn/mTM-align/

There are also more such services.

5a In Pfam database https://pfam.xfam.org/ use sequence search service. Include the table with domains and graphical representation of the domain architecture into your report.

5b Go (by clicking) to the page of the domain. See the link architecture.