Exercise M14

Exercise 1

In silico simulation of molecular biology experiments. Go to http://insilico.ehu.es/ and obtain in silico fingerprints for Burkholderia cenocepacia AU1054 with as many techniques as possible.

Exercise 2

Go to the MLST website http://www.mlst.net and figure out whether strain M87-7F clusters with the pneumococcal reference set (i.e. is very likely to be a pneumococcus) or clusters away from the reference set and is therefore unlikely to be a pneumococcus. Use both the allelic profiles and the concatenated sequences.
  • go to the MLST website and select the S. pneumoniae database (http://spneumoniae.mlst.net/)
  • download the entire database as Excel or Access file and obtain the sequences and allelic profile for M87-7F
  • follow the “Is it a pneumo?” link
  • enter the allelic profile and construct a tree
  • alternatively, enter the sequences and construct a tree
  • evaluate your results – i.e. compare your tree to the reference tree found at http://spneumoniae.mlst.net/misc/ntflash.asp#