Comparative Microbial Genomics and Taxonomy
>> Exercise M7
Bioinformatics: An Interactive Introduction to NCBI
Sequence searching and BLAST
Retrieve all data from a given organism or taxon
"Taxonomy at the click of a mouseÂ Â start at
and browse around! How many validly described Burkholderia, Ralstonia and Pandoraea species are there now?
RIDOM - Ribosomal Differentiation of Medical Microorganisms
retrieve sequence AJ239304 from GenBank
using RIDOM, determine from which species this sequence comes
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) Â suggestion : start at
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).
go to GenBank and retrieve the sequence (
BLAST the sequence (
align the sequences with ClustalW (
). Take some time to familiarise yourself with this tool!
construct a tree with Clustal and compare the result with the result obtained with BLAST
This file was last modified Tuesday 4th 2013f June 2013 11:49:20 GMT
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