BME 230: Computational Genomics

Student Genome Browsers

Under the "Browser" Column, there is a direct link to each genome browser.  They are starting out blank, and it is your mission to fill them in with your own genome analysis as part of the homework assignments for the course.  Up to 5% extra course credit will be given for going above and beyond regular assignments to increase the value of the browser to your genome's community.

At the completion of the course, well-constructed browsers will become part of the Santa Cruz family of genome browsers (of course, full credit will be given to its creator).

To get started filling in tracks on your browser, go to the top-level browser page on genome-test.cse.ucsc.edu, select "Archaea" or "Bacteria" under the "genome" menu, select your species under the "assembly" menu, the click on the "Add Your Own Custom Tracks" button.  More details are given on how to reformat your genomic analysis data to suit one of the browser formats.

An easy first track to start with is "Genbank" annotation, which can be extracted from the Genbank file you downloaded in your first homework.  This will help put your own independent analysis in context (i.e. did you find a new gene with your method, or does it conflict with prior annotation?)

Good luck & have fun!

Student   
Genome Species
  Browser 
Charles
Aquifex aeolicus VF5
 [Link]
Bernard
Buchnera sp. APS 
 [Link]
Chad
Vibrio cholerae  [Link]
Janaki
Methanococcus maripaludis S2  
 [Link]
Martina
Bordetella bronchiseptica RB50
 [Link]
Corey
Deinococcus radiodurans R1
 [Link]
Nick
Salmonella typhimurium LT2
 [Link]
Aleksey
Methanopyrus kandleri AV19    
 [Link]
Bret
Aeropyrum pernix
 [Link]
Fima
Escherichia coli O157:H7
 [Link]
John M.
Thermoplasma acidophilum
 [Link]
Kevin
Sulfolobus tokodaii
 [Link]
Rocky
Pyrococcus horikoshii
 [Link]
Brian
Geobacter sulfurreducens PCA
 [Link]
Patricia
Halobacterium sp. NRC-1
 [Link]
Todd
Helicobacter pylori, strain J99 [Link]