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Biological Sequence Analysis : Tools for Comparative Genomics

A List of Resources for the Presentation:

"Biological Sequence Analysis : Tools for Comparative Genomics",  HSCBB11 workshop "Advanced Bioinformatics Tools & Applications", Patras, 06/10/2011.

 

Note: The presentation is available to participants through the private workshop website. Unfortunately, some unpublished results had to be removed from the uploaded version. If you are really interested, please drop me an email.

 

IMG Data Management & Analysis Systems

http://img.jgi.doe.gov/

Microbial Genomes and Metagenomes collection:
http://img.jgi.doe.gov/cgi-bin/m/main.cgi

Some interesting routes to follow:

Find Genomes -> Genome Browser -> View Phylogenetically

Find Genomes -> Genome Search (try "Escherichia" as a query)

Case study: E. coli - K12 variants with complete genomes.

Preliminary analysis (<2mins)

  1. How many?

  2. Select and add to cart.

  3. Compare in terms of genome size / gene number.

  4. Try steps 1-3 with non K12 strains as well.

  5. ??

Getting deeper into the genome: E. coli K-12, MG1655 (~10mins)

Identify different types of information provided for this genome.

  1. Can you identify when/where was a peer-reviewed paper describing this genome was published?

  2. Depending on your field of interest, pick one of the Genome/Gene statistics and describe why it is important to know so.

Other related IMG tools: Contigs - Chromosome maps - Phylogenetic Distribution of Genes (I really like this one :-))

Find Genes -> Phylogenetic Profilers

Exploring phylogenetic profiles (~30 mins)

  1. Find the number all species/strain specific genes.
  2. Find the number of genes of the -- so called -- E. coli pangenome.
  3. Can you speculate what do these gene classes facilitate?

Compare Genomes -> Synteny Viewers -> Vista

 

Other interesting online tools - resources

http://genome.lbl.gov/vista/index.shtml

http://www.jcvi.org/cms/research/software/

...

 



by Dr. Radut.