Exercise M7

Exercise 1

Bioinformatics: An Interactive Introduction to NCBI

Exercise 2

Retrieve all data from a given organism or taxon http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/InfoHubs/Exercises/infohubs_qa_taxon.html

Exercise 3

"Taxonomy at the click of a mouse” – start at http://ijs.sgmjournals.org/misc/related.shtml and browse around! How many validly described Burkholderia, Ralstonia and Pandoraea species are there now?

Exercise 4

RIDOM - Ribosomal Differentiation of Medical Microorganisms http://www.ridom-rdna.de/
  • retrieve sequence AJ239304 from GenBank
  • using RIDOM, determine from which species this sequence comes

Exercise 5

Burkholderia genomics : compile a list of all Burkholderia genomes that are being sequenced (provide source, GC content, genome size and estimated no. of genes for as much genomes as possible) – suggestion : start at http://www.genomesonline.org or http://www.cbs.dtu.dk/services/GenomeAtlas/

Exercise 6

What are the closest phylogenetic neighbours of strain R-23533? The accession no. of its 16S rRNA sequence is AJ871398. Draw a tree of this sequence and the sequence of the 16S rRNA gene of the 8 most related species (not sequences).