Continuation from class 10

• blast and commandline blast (the slides cotain links that only become accessible, after you switched to presentation mode)

ELSE

• Where to get genomes: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ (check out different files (.faa .fna .ffn .ptt) using A. veronii and A. salmonicida as example)
• discuss blastall, example analysis for pairwise genome comparison is here (discuss %identity, alignment lengthd, #of identical aa)
• example of what one could do with this:
  • (perl script to extract top scoring hits is here)
  • (perl script to replace gi number with position on the genome is here)
  • (perl script to make gnuplot is here, output is here)

sequence space