Gene plot Frankia ACN vs Frankia CCI3

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Presentation transcript:

Gene plot Frankia ACN vs Frankia CCI3 More info on these strains at Philippe Normand, Pascal Lapierre, Louis S. Tisa, Johann Peter Gogarten, Nicole Alloisio, Emilie Bagnarol, Carla A. Bassi, Alison M. Berry, Derek M. Bickhart, Nathalie Choisne, Arnaud Couloux, Benoit Cournoyer, Stephane Cruveiller, Vincent Daubin, Nadia Demange, Maria Pilar Francino, Eugene Goltsman, Ying Huang, Olga R. Kopp, Laurent Labarre, Alla Lapidus, Celine Lavire, Joelle Marechal, Michele Martinez, Juliana E. Mastronunzio, Beth C. Mullin, James Niemann, Pierre Pujic, Tania Rawnsley, Zoe Rouy, Chantal Schenowitz, Anita Sellstedt, Fernando Tavares, Jeffrey P. Tomkins, David Vallenet, Claudio Valverde, Luis G. Wall, Ying Wang, Claudine Medigue, and David R. Benson (2007): Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Research 17: 7-15

Part of Perl script to keep only top scoring blast hit for each query

Part of the Frankia CCI3 ptt file

Part of the Frankia CCI3 ptt file This time in MSWord, with tabs set so it aligns nicely – note the non printing characters in blue

Add numbers to faa file – script Read header of table

Add numbers to faa file –script Read table to hash $part[3] contains the GI number

Add numbers to faa file –script Read, modify, write faa file

Plot blast.out

Location of blast hits in the two genomes E-value <10^-24:

Plot blast.out and blast.out.top #Note: gnuplot only runs on master node

Location of all blast hits in the two genomes and location of all top scoring blast hits in the two genomes E-value <10^-24:

Location of all blast hits in the two genomes and location of all top scoring blast hits in the two genomes E-value <10^-50:

Location of all blast hits in the two genomes and location of all top scoring blast hits in the two genomes E-value <10^-7:

Aeromonas_hydrophila_ATCC_7966_uid58617 versus Aeromonas_hydrophila_ML09_119_uid205540/ Evalue cut off: 10^-4

E-value cut off: 10^-4 Top-scoring hits only Aeromonas_hydrophila_ATCC_7966_uid58617 versus Aeromonas_hydrophila_ML09_119_uid205540/ E-value cut off: 10^-4 Top-scoring hits only

Top scoring hit % identity versus position Aeromonas_hydrophila_ATCC_7966_uid58617 versus Aeromonas_hydrophila_ML09_119_uid205540/ Top scoring hit % identity versus position

Top scoring hit bitscore per aa versus position Aeromonas_hydrophila_ATCC_7966_uid58617 versus Aeromonas_hydrophila_ML09_119_uid205540/ Top scoring hit bitscore per aa versus position

Aeromonas_hydrophila_ATCC_7966_uid58617 versus Aeromonas_hydrophila_ML09_119_uid205540/ Top scoring hit bitscore per aa versus position and log (E-value+10^-150)